CELF1

Summary

CELF1 (CUGBP Elav-like family member 1, HGNC:2549) is a protein-coding gene on chromosome 11p11.2, encoding CUGBP Elav-like family member 1 (Q92879). RNA-binding protein implicated in the regulation of several post-transcriptional events.

Members of the CELF/BRUNOL protein family contain two N-terminal RNA recognition motif (RRM) domains, one C-terminal RRM domain, and a divergent segment of 160-230 aa between the second and third RRM domains. Members of this protein family regulate pre-mRNA alternative splicing and may also be involved in mRNA editing, and translation. This gene may play a role in myotonic dystrophy type 1 (DM1) via interactions with the dystrophia myotonica-protein kinase (DMPK) gene. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 10658 — RefSeq curated summary.

At a glance

• GWAS associations: 55
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_001376376

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2549
Approved symbol	CELF1
Name	CUGBP Elav-like family member 1
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	CUG-BP, hNab50, BRUNOL2, NAB50, CUGBP, NAPOR, EDEN-BP
Ensembl gene	ENSG00000149187
Ensembl biotype	protein_coding
OMIM	601074
Entrez	10658

Gene structure

Transcript identifiers

Ensembl transcripts: 33 — 27 protein_coding, 4 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000310513, ENST00000358597, ENST00000361904, ENST00000395290, ENST00000395292, ENST00000422993, ENST00000524648, ENST00000525841, ENST00000526277, ENST00000526419, ENST00000528434, ENST00000528538, ENST00000530151, ENST00000531165, ENST00000532048, ENST00000532146, ENST00000534614, ENST00000535982, ENST00000539254, ENST00000539455, ENST00000543178, ENST00000687097, ENST00000871685, ENST00000871686, ENST00000871687, ENST00000871688, ENST00000871689, ENST00000871690, ENST00000871691, ENST00000949348, ENST00000949349, ENST00000949350, ENST00000949351

RefSeq mRNA: 91 — MANE Select: NM_001376376 NM_001025596, NM_001172639, NM_001172640, NM_001330272, NM_001376369, NM_001376370, NM_001376371, NM_001376372, NM_001376373, NM_001376374, NM_001376375, NM_001376376, NM_001376377, NM_001376378, NM_001376379, NM_001376380, NM_001376381, NM_001376382, NM_001376383, NM_001376384, NM_001376385, NM_001376386, NM_001376387, NM_001376388, NM_001376389, NM_001376390, NM_001376391, NM_001376393, NM_001376395, NM_001376396, NM_001376397, NM_001376399, NM_001376406, NM_001376407, NM_001376408, NM_001376409, NM_001376410, NM_001376411, NM_001376412, NM_001376413, NM_001376414, NM_001376415, NM_001376417, NM_001376418, NM_001376419, NM_001376420, NM_001376421, NM_001376422, NM_001376423, NM_001376424, NM_001376425, NM_001376426, NM_001376427, NM_001376428, NM_001376429, NM_001376430, NM_001376431, NM_001376432, NM_001376433, NM_001376434, NM_001376435, NM_001376436, NM_001376437, NM_001376438, NM_001376439, NM_001376440, NM_001376441, NM_001376442, NM_001376443, NM_001376444, NM_001376445, NM_001376446, NM_001376447, NM_001376448, NM_001376449, NM_001376450, NM_001376451, NM_001376452, NM_001376453, NM_001376454, NM_001376455, NM_001376456, NM_001376457, NM_001376458, NM_001376459, NM_001376460, NM_001376461, NM_001376462, NM_001376463, NM_006560, NM_198700

CCDS: CCDS31482, CCDS53622, CCDS53623, CCDS7938, CCDS7939, CCDS81565

Canonical transcript exons

ENST00000687097 — 15 exons

Exon	Start	End
ENSE00001098102	47477297	47477425
ENSE00001624279	47483453	47483532
ENSE00001704133	47486750	47486798
ENSE00002184843	47500861	47500932
ENSE00003528217	47478877	47478952
ENSE00003609891	47488837	47489024
ENSE00003616977	47482695	47482856
ENSE00003631635	47475336	47475521
ENSE00003660178	47484389	47484523
ENSE00003689551	47473088	47473231
ENSE00003693230	47499453	47499604
ENSE00003694698	47476846	47476959
ENSE00003790483	47487159	47487241
ENSE00003926150	47465937	47472357
ENSE00003927211	47552992	47553132

Expression profiles

Bgee: expression breadth ubiquitous, 300 present calls, max score 99.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.0435 / max 253.7529, expressed in 1821 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119637	28.7110	1817
119638	2.9352	1570
119623	1.8930	1107
119639	1.8053	1165
119622	1.7230	1130
119621	1.4535	821
119634	0.4145	191
119636	0.3476	146
119632	0.2169	86
119626	0.1904	70

Top tissues by expression

300 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.25	gold quality
cauda epididymis	UBERON:0004360	99.18	gold quality
caput epididymis	UBERON:0004358	99.06	gold quality
oocyte	CL:0000023	98.97	gold quality
corpus epididymis	UBERON:0004359	98.94	gold quality
adult organism	UBERON:0007023	98.82	gold quality
renal medulla	UBERON:0000362	98.74	gold quality
trabecular bone tissue	UBERON:0002483	98.67	gold quality
pylorus	UBERON:0001166	98.64	gold quality
seminal vesicle	UBERON:0000998	98.63	gold quality
mucosa of paranasal sinus	UBERON:0005030	98.63	gold quality
bronchial epithelial cell	CL:0002328	98.62	gold quality
visceral pleura	UBERON:0002401	98.61	gold quality
cardia of stomach	UBERON:0001162	98.45	gold quality
CA1 field of hippocampus	UBERON:0003881	98.41	gold quality
epithelium of bronchus	UBERON:0002031	98.34	gold quality
bronchus	UBERON:0002185	98.34	gold quality
nipple	UBERON:0002030	98.28	gold quality
lateral globus pallidus	UBERON:0002476	98.27	gold quality
saphenous vein	UBERON:0007318	98.26	gold quality
superficial temporal artery	UBERON:0001614	98.22	gold quality
cranial nerve II	UBERON:0000941	98.14	gold quality
pleura	UBERON:0000977	98.05	gold quality
mammary duct	UBERON:0001765	98.02	gold quality
cerebellar vermis	UBERON:0004720	98.02	gold quality
oral cavity	UBERON:0000167	98.01	gold quality
body of tongue	UBERON:0011876	97.98	gold quality
superior surface of tongue	UBERON:0007371	97.97	gold quality
parietal pleura	UBERON:0002400	97.91	gold quality
type B pancreatic cell	CL:0000169	97.90	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
ABCA1	Repression
AIFM1	Activation
TP53	Activation

Upstream regulators (CollecTRI, top): CEBPB, E2F1, MYOG

miRNA regulators (miRDB)

79 targeting CELF1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-589-3P	99.91	69.62	2088

Literature-anchored findings (GeneRIF, showing 40)

• CUGBP1 induces the translation of p21 via binding to a GC-rich sequence located within the 5’ region of p21 mRNA. Alterations in the activity of CUGBP1 causes disruption of p21-dependent control of cell cycle arrest. (PMID:11564876)
• CUG-BP and Xenopus EDEN-BP have very similar RNA-binding specificities; it is suggested that the CUG expansion associated with Type 1 myotonic dystrophy can affect the function of CUG-BP, leading to a trans-dominant effect on normal RNA processing (PMID:12799066)
• Data show that epidermal growth factor receptor signaling results in phosphorylation of CUG-BP1, and leads to increased binding of CUG-BP1 to CCAAT/enhancer binding protein beta (C/EBP beta) mRNA and elevated expression of the C/EBPbeta LIP isoform. (PMID:15082764)
• The results of this study suggest that the CUG expansion may bind to complementary sequences within the CUGBP1 mRNA and that this molecular interaction may affect CUGBP1 mRNA expression in DM1. (PMID:15099703)
• CUG-BP, therefore, is the first RNA-binding protein shown to directly recruit a deadenylase to an RNA substrate.CUG-BP interacts with PARN in extracts by coimmunoprecipitation, and this interaction can be recapitulated using recombinant proteins (PMID:16601207)
• coordinated physical and functional interactions between hnRNP H, CUG-BP1 and MBNL1 dictate IR splicing in normal and DM1 myoblasts (PMID:16946708)
• transcription of Cugbp1 gene in muscle is regulated by myogenin and E proteins (PMID:17531403)
• Insertional disruption of the CUGBP1 gene is associated with leukemogenesis (PMID:17854664)
• Data show that expression of DMPK-CUG-repeat RNA results in hyperphosphorylation and stabilization of CUGBP1, and suggest that inappropriate activation of the PKC pathway contributes to the pathogenic effects of a noncoding RNA. (PMID:17936705)
• CUG-BP1 specifically recognized UG repeats, probably through cooperative binding of RNA recognition motifs at both ends of the protein. (PMID:18039683)
• These results demonstrate the dynamic behavior of CUGBP-1 during stress response and that the linker region, in concert with RRMs, plays a significant role in defining its subcellular localization and dynamics. (PMID:18164289)
• the GRE mediates coordinated mRNA decay by binding to CUGBP1. (PMID:18243120)
• Results show that ectopic expression of cyclin D3 corrects differentiation of DM1 myoblasts through activation of CUGBP1. (PMID:18570922)
• SRp20, SF2/ASF, and CUG-BP1 act antagonistically to regulate IR alternative splicing in vivo and that the relative ratios of SRp20 and SF2/ASF to CUG-BP1 in different cells determine the degree of exon inclusion. (PMID:19047369)
• CUG-BP1 and HuR act as factors that bind to the SBP2 3’ UTR, which suggests that TTR-RBPs play a role in the regulation of SBP2 (PMID:19106619)
• This study revealed the unique mechanism that enables the CUG-BP1 RNA-recognition motif 3 to discriminate the short RNA segment from other sequences. (PMID:19553194)
• These results strongly support a role for CUGBP1 up-regulation in myotonic dystrophy type 1 pathogenesis. (PMID:20051426)
• CUGBP1 directly controls CD9 expression. (PMID:20227387)
• identified 613 putative mRNA targets of CUGBP1 and found that the UGUUUGUUUGU GU-rich elements (GREs) sequence and a GU-repeat sequence were both highly enriched in the 3’ UTRs of these targets (PMID:20547756)
• Overexpression of CUGBP1 in mouse skeletal muscle reproduces features of myotonic dystrophy type 1. (PMID:20603324)
• Data show that crystal structures of CUGBP1 RRM1 and tandem RRM1/2 domains bound to RNAs containing tandem UGU(U/G) elements. (PMID:20947024)
• CUG-binding protein represses translation of p27Kip1 mRNA through its internal ribosomal entry site (PMID:21508681)
• Stress granules component CUGBP1 was identified as a factor required for p21 mRNA stabilization. (PMID:21637851)
• CUGBP1 binding to certain GRE-containing target transcripts decreased following T cell activation through activation-dependent phosphorylation of CUGBP1. (PMID:22117072)
• study suggests that regulation of CUGBP1 and MBNL1 is essential for accurate control of destabilization of a broad spectrum of mRNAs as well as of alternative splicing events (PMID:22355723)
• CUG-BP1 is overexpressed in oesophageal cancer cell lines and human oesophageal cancer specimens. CUG-BP1 associates with the 3’-untranslated region of survivin mRNA. (PMID:22646166)
• The results suggest that CUG-BP1 binds to nucleotides 51-100 of the human albumin 3’UTR. In human cells CUG-BP1 binding may thus play a role in regulation of albumin expression and, additionally, it may have a function in post-transcriptional control in CHO cells. (PMID:22982313)
• CUGBP1 represses occludin translation by increasing occludin mRNA recruitment to P-bodies. (PMID:23155001)
• CELF1 depletion induces apoptosis in tumor cells, but not in normal cells. (PMID:23324604)
• High CUGBP1 expression is associated with non-small cell lung cancer. (PMID:23359188)
• CUGBP1 seems to play a role in classic DM1 but not in DM2 (PMID:24376746)
• CUGBP1 was expressed in 85.7% hepatocellular carcinoma specimens compared with 50% in normal liver specimens. CUGBP1 silencing remarkably decreased the proliferation of HepG2 cells. (PMID:24502807)
• The Alzheimer’s disease single nucleotide polymorphism rs10838725 (pAD = 1.1 x 10(-08)) at the locus CELF1 is also genome-wide significant for obesity. (PMID:24788522)
• the size and the number of colonies formed in gastric cancer MGC-803 cells were markedly reduced in the absence of CUGBP1 (PMID:24818870)
• CUGBP1 has a critical role in modulating cell growth and apoptosis (PMID:25077823)
• Data suggest a model for RNA binding protein CELF1/CUGBP1-mediated regulation of alternative polyadenylation (APA). (PMID:25123787)
• The result is consistent with the hypothesis that MBNL proteins are trapped by expanded CUG repeats and inactivated in myotonic dystrophy type 1 (DM1) and that CELF1 is activated in DM1. (PMID:25403273)
• These results demonstrate the importance of CUGBP1 in the biological and pathological functions of NSCLC and indicate its potential as a therapeutic target for NSCLC. (PMID:25619475)
• CUGBP1 promotes cell proliferation and suppresses apoptosis via down-regulating C-EBPalpha in human non-small cell lung cancers. (PMID:25701464)
• The results indicate that the cellular level of miR-122 is determined by the balance between the opposing effects of GLD-2 and PARN/CUGBP1 on the metabolism of its 3’-terminus. (PMID:26130707)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	celf1	ENSDARG00000005315
mus_musculus	Celf1	ENSMUSG00000005506
rattus_norvegicus	Celf1	ENSRNOG00000010379
drosophila_melanogaster	bru1	FBGN0000114
drosophila_melanogaster	Pof	FBGN0035047
drosophila_melanogaster	bru2	FBGN0262475
caenorhabditis_elegans		WBGENE00017135
caenorhabditis_elegans		WBGENE00017140
caenorhabditis_elegans		WBGENE00020354

Paralogs (6): CELF2 (ENSG00000048740), CELF4 (ENSG00000101489), RBM28 (ENSG00000106344), CELF6 (ENSG00000140488), CELF3 (ENSG00000159409), CELF5 (ENSG00000161082)

Protein

Protein identifiers

CUGBP Elav-like family member 1 — Q92879 (reviewed: Q92879)

Alternative names: 50 kDa nuclear polyadenylated RNA-binding protein, Bruno-like protein 2, CUG triplet repeat RNA-binding protein 1, CUG-BP- and ETR-3-like factor 1, Deadenylation factor CUG-BP, Embryo deadenylation element-binding protein homolog, RNA-binding protein BRUNOL-2

All UniProt accessions (10): Q92879, E9PKA1, E9PKU1, E9PQK4, E9PSH0, F5H0D8, F5H3J7, F5H4Y5, F5H7M7, G5EA30

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein implicated in the regulation of several post-transcriptional events. Involved in pre-mRNA alternative splicing, mRNA translation and stability. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. Specifically activates exon 5 inclusion of cardiac isoforms of TNNT2 during heart remodeling at the juvenile to adult transition. Acts both as an activator and as a repressor of a pair of coregulated exons: promotes inclusion of the smooth muscle (SM) exon but exclusion of the non-muscle (NM) exon in actinin pre-mRNAs. Activates SM exon 5 inclusion by antagonizing the repressive effect of PTB. Promotes exclusion of exon 11 of the INSR pre-mRNA. Inhibits, together with HNRNPH1, insulin receptor (IR) pre-mRNA exon 11 inclusion in myoblast. Increases translation and controls the choice of translation initiation codon of CEBPB mRNA. Increases mRNA translation of CEBPB in aging liver. Increases translation of CDKN1A mRNA by antagonizing the repressive effect of CALR3. Mediates rapid cytoplasmic mRNA deadenylation. Recruits the deadenylase PARN to the poly(A) tail of EDEN-containing mRNAs to promote their deadenylation. Required for completion of spermatogenesis. Binds to (CUG)n triplet repeats in the 3’-UTR of transcripts such as DMPK and to Bruno response elements (BREs). Binds to muscle-specific splicing enhancer (MSE) intronic sites flanking the alternative exon 5 of TNNT2 pre-mRNA. Binds to AU-rich sequences (AREs or EDEN-like) localized in the 3’-UTR of JUN and FOS mRNAs. Binds to the IR RNA. Binds to the 5’-region of CDKN1A and CEBPB mRNAs. Binds with the 5’-region of CEBPB mRNA in aging liver. May be a specific regulator of miRNA biogenesis. Binds to primary microRNA pri-MIR140 and, with CELF2, negatively regulates the processing to mature miRNA.

Subunit / interactions. Component of an EIF2 complex at least composed of CELF1/CUGBP1, CALR, CALR3, EIF2S1, EIF2S2, HSP90B1 and HSPA5. Associates with polysomes. Interacts with HNRNPH1; the interaction in RNA-dependent. Interacts with PARN.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Ubiquitous.

Post-translational modifications. Phosphorylated. Its phosphorylation status increases in senescent cells.

Domain organisation. RRM1 and RRM2 domains preferentially target UGU(U/G)-rich mRNA elements.

Induction. Up-regulated in myotonic dystrophy pathophysiology (DM).

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the CELF/BRUNOL family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q92879-1	1, LYLQ	yes
Q92879-2	2
Q92879-3	3, A
Q92879-4	4
Q92879-5	5
Q92879-6	6

RefSeq proteins (91): NP_001020767, NP_001166110, NP_001166111, NP_001317201, NP_001363298, NP_001363299, NP_001363300, NP_001363301, NP_001363302, NP_001363303, NP_001363304, NP_001363305, NP_001363306, NP_001363307, NP_001363308, NP_001363309, NP_001363310, NP_001363311, NP_001363312, NP_001363313, NP_001363314, NP_001363315, NP_001363316, NP_001363317, NP_001363318, NP_001363319, NP_001363320, NP_001363322, NP_001363324, NP_001363325, NP_001363326, NP_001363328, NP_001363335, NP_001363336, NP_001363337, NP_001363338, NP_001363339, NP_001363340, NP_001363341, NP_001363342, NP_001363343, NP_001363344, NP_001363346, NP_001363347, NP_001363348, NP_001363349, NP_001363350, NP_001363351, NP_001363352, NP_001363353, NP_001363354, NP_001363355, NP_001363356, NP_001363357, NP_001363358, NP_001363359, NP_001363360, NP_001363361, NP_001363362, NP_001363363, NP_001363364, NP_001363365, NP_001363366, NP_001363367, NP_001363368, NP_001363369, NP_001363370, NP_001363371, NP_001363372, NP_001363373, NP_001363374, NP_001363375, NP_001363376, NP_001363377, NP_001363378, NP_001363379, NP_001363380, NP_001363381, NP_001363382, NP_001363383, NP_001363384, NP_001363385, NP_001363386, NP_001363387, NP_001363388, NP_001363389, NP_001363390, NP_001363391, NP_001363392, NP_006551, NP_941989 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR034196	CELF1/2_RRM1	Domain
IPR034198	CELF1/2_RRM2	Domain
IPR034199	CELF1/2_RRM3	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076

UniProt features (51 total): strand 16, helix 11, splice variant 5, turn 5, modified residue 4, domain 3, mutagenesis site 3, chain 1, cross-link 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

8 structures.

PDB	Method	Resolution (Å)
3NMR	X-RAY DIFFRACTION	1.85
3NNA	X-RAY DIFFRACTION	1.9
3NNC	X-RAY DIFFRACTION	2.2
3NNH	X-RAY DIFFRACTION	2.75
2CPZ	SOLUTION NMR
2DHS	SOLUTION NMR
2RQ4	SOLUTION NMR
2RQC	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92879-F1	68.17	0.21

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (5): 109, 1, 4, 179, 302

Mutagenesis-validated functional residues (3):

Position	Phenotype
63	does not reduce rna-binding; when associated with d-331 and f-472. abolishes are/eden-dependent deadenylation; when asso
331	does not reduce rna-binding; when associated with l-63 and f-472. abolishes are/eden-dependent deadenylation; when assoc
472	does not reduce rna-binding; when associated with l-63 and d-331. abolishes are/eden-dependent deadenylation; when assoc

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 272 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, MULLIGHAN_NPM1_SIGNATURE_3_UP, DORSAM_HOXA9_TARGETS_UP, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOBP_INFLAMMATORY_RESPONSE, GOBP_ALTERNATIVE_MRNA_SPLICING_VIA_SPLICEOSOME, GCM_ZNF198, MAZ_Q6, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GCM_PPM1D, AREB6_01, GOBP_NEGATIVE_REGULATION_OF_TRANSLATION, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSLATION_REGULATOR_ACTIVITY

GO Biological Process (18): regulation of alternative mRNA splicing, via spliceosome (GO:0000381), mRNA splice site recognition (GO:0006376), mRNA processing (GO:0006397), germ cell development (GO:0007281), negative regulation of cell population proliferation (GO:0008285), embryo development ending in birth or egg hatching (GO:0009792), positive regulation of gene expression (GO:0010628), negative regulation of gene expression (GO:0010629), post-transcriptional gene silencing (GO:0016441), regulatory ncRNA-mediated post-transcriptional gene silencing (GO:0035194), regulation of RNA splicing (GO:0043484), regulation of inflammatory response (GO:0050727), mRNA destabilization (GO:0061157), spermatid development (GO:0007286), RNA splicing (GO:0008380), negative regulation of translation (GO:0017148), cerebral cortex development (GO:0021987), positive regulation of multicellular organism growth (GO:0040018)

GO Molecular Function (10): mRNA regulatory element binding translation repressor activity (GO:0000900), RNA binding (GO:0003723), mRNA binding (GO:0003729), mRNA 3’-UTR binding (GO:0003730), pre-mRNA binding (GO:0036002), BRE binding (GO:0042835), nucleic acid binding (GO:0003676), protein binding (GO:0005515), translation initiation factor binding (GO:0031369), lncRNA binding (GO:0106222)

GO Cellular Component (8): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytoplasmic stress granule (GO:0010494), membrane (GO:0016020), perinucleolar compartment (GO:0097356), ribonucleoprotein complex (GO:1990904), male germ cell nucleus (GO:0001673)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA binding	4
cellular anatomical structure	4
regulation of gene expression	3
negative regulation of gene expression	3
RNA processing	2
gene expression	2
mRNA binding	2
binding	2
nuclear lumen	2
alternative mRNA splicing, via spliceosome	1
regulation of mRNA splicing, via spliceosome	1
spliceosomal complex assembly	1
protein-RNA complex assembly	1
mRNA metabolic process	1
developmental process involved in reproduction	1
gamete generation	1
cellular process involved in reproduction in multicellular organism	1
cell development	1
cell population proliferation	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
embryo development	1
positive regulation of macromolecule biosynthetic process	1
negative regulation of macromolecule biosynthetic process	1
post-transcriptional regulation of gene expression	1
post-transcriptional gene silencing	1
regulatory ncRNA-mediated gene silencing	1
RNA splicing	1
regulation of primary metabolic process	1
inflammatory response	1
regulation of defense response	1
regulation of response to external stimulus	1
regulation of mRNA stability	1
RNA destabilization	1
positive regulation of mRNA catabolic process	1
germ cell development	1
spermatid differentiation	1
translation	1
regulation of translation	1
negative regulation of protein metabolic process	1

Protein interactions and networks

STRING

2160 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CELF1	MBNL1	Q9NR56	969
CELF1	CLCN1	P35523	931
CELF1	DMPK	Q09013	925
CELF1	CEBPD	P49716	908
CELF1	MBNL2	Q5VZF2	906
CELF1	MBNL3	Q9NUK0	900
CELF1	EIF2S1	P05198	869
CELF1	PTBP1	P26599	862
CELF1	CNBP	P20694	825
CELF1	TNNT2	P45379	820
CELF1	PURA	Q00577	792
CELF1	HNRNPH2	P55795	770
CELF1	HNRNPH1	P31943	763
CELF1	HNRNPA2B1	P22626	731
CELF1	KHSRP	Q92945	725

IntAct

36 interactions, top by confidence:

A	B	Type	Score
HNRNPC	CELF1	psi-mi:“MI:0915”(physical association)	0.520
MBNL1	HNRNPH1	psi-mi:“MI:0914”(association)	0.500
HNRNPH1	CELF1	psi-mi:“MI:0915”(physical association)	0.400
CELF1	RALY	psi-mi:“MI:0915”(physical association)	0.370
	BAG6	psi-mi:“MI:0914”(association)	0.350
USP10	EIF4G3	psi-mi:“MI:0914”(association)	0.350
pipB2	PSMD12	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
MSI1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
	GTPBP10	psi-mi:“MI:0914”(association)	0.350
PRKY	METTL15	psi-mi:“MI:0914”(association)	0.350
	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
	EIF3F	psi-mi:“MI:0914”(association)	0.350
NUP42		psi-mi:“MI:0914”(association)	0.350
HNRNPCL2	SMCHD1	psi-mi:“MI:0914”(association)	0.350
	RTCA	psi-mi:“MI:0914”(association)	0.350
	POLRMT	psi-mi:“MI:0914”(association)	0.350
RABIF	RAD21	psi-mi:“MI:0914”(association)	0.350
DND1	UBA6	psi-mi:“MI:0914”(association)	0.350
GAB2	UBA6	psi-mi:“MI:0914”(association)	0.350
MRPL49	UBA6	psi-mi:“MI:0914”(association)	0.350
PEX7	UBA6	psi-mi:“MI:0914”(association)	0.350
VENTX	UBA6	psi-mi:“MI:0914”(association)	0.350
PTBP3		psi-mi:“MI:0914”(association)	0.350
HNRNPC	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
LIN28B	MEX3A	psi-mi:“MI:2364”(proximity)	0.270
NONO	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
QKI	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
UTP3	NACA	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (328): CELF1 (Affinity Capture-MS), CELF1 (Co-fractionation), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-RNA), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS), CELF1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2P872, A1L1C7, A4IIM2, B2RYD2, F1LQ48, O57406, O88532, O95319, P14866, P28659, P51513, P57723, P57724, Q28HE9, Q2PFW9, Q32PX7, Q3U0V1, Q3US41, Q4QQT3, Q4R535, Q58A45, Q5F3T7, Q5NVC8, Q5R8Y8, Q5R995, Q5U231, Q640Q5, Q6DGV1, Q6GPM1, Q6NXG1, Q6P0B1, Q6PF35, Q792H5, Q7T2T1, Q7TSY6, Q7ZXE2, Q80WA4, Q8R081, Q8UVD9, Q91WJ8

Diamond homologs: A0A0D1DWZ5, A0JM51, A1CRM1, A1D4K4, A2A5N3, A2Q848, A3LXL0, A4IIM2, A4QUF0, A5DW14, F4HT49, O04319, O14102, O22173, O57406, O64380, O95319, O97018, P04147, P0CB38, P0CP46, P0CP47, P20965, P21187, P28659, P29558, P31209, P32588, P39697, P42731, P60047, P60048, P60049, P60050, Q08E07, Q09442, Q0CR95, Q0U1G2, Q13310, Q15427

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
AKT1	“up-regulates activity”	CELF1	phosphorylation
AKT	“up-regulates activity”	CELF1	phosphorylation
CDK4	“up-regulates activity”	CELF1	phosphorylation
CELF1	“up-regulates activity”	EIF2S1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

60 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1564 predictions. Top by Δscore:

Variant	Effect	Δscore
11:47473083:CATA:C	donor_loss	1.0000
11:47473084:ATACC:A	donor_loss	1.0000
11:47473085:TACCA:T	donor_loss	1.0000
11:47473086:A:C	donor_loss	1.0000
11:47473244:C:CT	acceptor_gain	1.0000
11:47473244:C:T	acceptor_gain	1.0000
11:47473245:A:T	acceptor_gain	1.0000
11:47475331:CTCA:C	donor_loss	1.0000
11:47475332:TCA:T	donor_loss	1.0000
11:47475333:CACCT:C	donor_loss	1.0000
11:47475334:ACCTT:A	donor_gain	1.0000
11:47475335:C:CA	donor_loss	1.0000
11:47475335:CCTTC:C	donor_gain	1.0000
11:47475338:T:A	donor_gain	1.0000
11:47475517:CATTC:C	acceptor_gain	1.0000
11:47475518:ATTC:A	acceptor_gain	1.0000
11:47475519:TTC:T	acceptor_gain	1.0000
11:47475520:TCC:T	acceptor_loss	1.0000
11:47475521:CC:C	acceptor_loss	1.0000
11:47475521:CCT:C	acceptor_gain	1.0000
11:47475522:C:T	acceptor_gain	1.0000
11:47475523:T:C	acceptor_gain	1.0000
11:47475523:T:TC	acceptor_gain	1.0000
11:47475527:T:C	acceptor_gain	1.0000
11:47475527:T:TC	acceptor_gain	1.0000
11:47477291:GCTTA:G	donor_loss	1.0000
11:47477292:CTTA:C	donor_loss	1.0000
11:47477293:TTA:T	donor_loss	1.0000
11:47477294:TAC:T	donor_loss	1.0000
11:47477295:A:AT	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000007034 (11:47524641 G>A), RS1000010728 (11:47560793 T>C), RS1000068775 (11:47481253 G>A,C), RS1000098771 (11:47513172 C>A), RS1000149468 (11:47512779 A>C), RS1000155685 (11:47547760 A>C), RS1000187412 (11:47495650 A>G), RS1000190726 (11:47507853 G>A,C), RS1000200693 (11:47565230 G>A), RS1000213120 (11:47547981 A>C,T), RS1000225583 (11:47470439 G>A,C), RS1000242298 (11:47488402 G>A), RS1000261307 (11:47494791 C>A,T), RS1000270283 (11:47501492 A>G), RS1000300001 (11:47501663 A>C,G,T)

Disease associations

OMIM: gene MIM:601074 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

55 associations (top):

Study	Trait	p-value
GCST000830_15	Body mass index	2.000000e-12
GCST002245_16	Alzheimer’s disease (late onset)	1.000000e-08
GCST004557_101	Body mass index	3.000000e-07
GCST004557_137	Body mass index	7.000000e-07
GCST004557_19	Body mass index	1.000000e-11
GCST004557_202	Body mass index	8.000000e-07
GCST004557_231	Body mass index	5.000000e-12
GCST004557_63	Body mass index	2.000000e-06
GCST004558_134	Body mass index (joint analysis main effects and physical activity interaction)	7.000000e-06
GCST004558_151	Body mass index (joint analysis main effects and physical activity interaction)	2.000000e-11
GCST004558_16	Body mass index (joint analysis main effects and physical activity interaction)	6.000000e-11
GCST004558_173	Body mass index (joint analysis main effects and physical activity interaction)	5.000000e-06
GCST004558_99	Body mass index (joint analysis main effects and physical activity interaction)	5.000000e-06
GCST004559_14	Body mass index in physically active individuals	2.000000e-08
GCST004559_96	Body mass index in physically active individuals	4.000000e-09
GCST004628_44	Immature fraction of reticulocytes	5.000000e-09
GCST005232_56	Neuroticism	1.000000e-16
GCST005829_9	Hand grip strength	7.000000e-15
GCST005830_12	Hand grip strength	3.000000e-18
GCST005905_14	Global electrical heterogeneity phenotypes	6.000000e-09
GCST005984_53	Glomerular filtration rate	3.000000e-10
GCST006614_20	Total cholesterol levels	1.000000e-09
GCST006716_13	Alcohol use disorder (total score)	6.000000e-09
GCST006923_11	Loneliness	1.000000e-07
GCST006924_13	Loneliness (MTAG)	1.000000e-08
GCST007293_118	Body fat distribution (arm fat ratio)	3.000000e-08
GCST007293_19	Body fat distribution (arm fat ratio)	2.000000e-10
GCST007293_45	Body fat distribution (arm fat ratio)	5.000000e-14
GCST007294_28	Body fat distribution (trunk fat ratio)	6.000000e-09
GCST007294_9	Body fat distribution (trunk fat ratio)	4.000000e-06

EFO canonical traits (15, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0008002	physical activity measurement
EFO:0007986	reticulocyte count
EFO:0007660	neuroticism measurement
EFO:0006941	grip strength measurement
EFO:0004327	electrocardiography
EFO:0004574	total cholesterol measurement
EFO:0009458	alcohol use disorder measurement
EFO:0007865	loneliness measurement
EFO:0004341	body fat distribution
EFO:0010178	non-lobar intracerebral hemorrhage
EFO:0000195	metabolic syndrome
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

49 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression	3
Cyclosporine	decreases expression, increases methylation	3
sodium arsenate	decreases expression, increases abundance, increases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
Benzo(a)pyrene	decreases expression, affects methylation	2
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	increases expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
bisphenol A	increases methylation	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
cupric oxide	increases expression	1
nivalenol	increases expression	1
methacrylaldehyde	decreases expression, increases abundance, affects cotreatment	1
cyclic 3’,5’-uridine monophosphate	affects binding	1
tamibarotene	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	increases reaction, affects binding	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
LDN 193189	increases expression, affects cotreatment	1
Temozolomide	increases expression	1
Acetaminophen	increases expression	1
Acrolein	decreases expression, increases abundance, affects cotreatment	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Atrazine	increases expression	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Dinitrochlorobenzene	affects binding	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2U3	Abcam HEK293T CELF1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.