RBM44

Summary

RBM44 (RNA binding motif protein 44, HGNC:24756) is a protein-coding gene on chromosome 2q37.3, encoding RNA-binding protein 44 (Q6ZP01). Component of intercellular bridges during meiosis.

Predicted to enable protein homodimerization activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in cytoplasm and intercellular bridge. Predicted to be part of catalytic step 2 spliceosome.

Source: NCBI Gene 375316 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 144 total
• MANE Select transcript: NM_001080504

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24756
Approved symbol	RBM44
Name	RNA binding motif protein 44
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40411
Ensembl gene	ENSG00000177483
Ensembl biotype	protein_coding
OMIM	621038
Entrez	375316

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000316997, ENST00000409864, ENST00000444524, ENST00000480583, ENST00000491996

RefSeq mRNA: 1 — MANE Select: NM_001080504 NM_001080504

CCDS: CCDS46554

Canonical transcript exons

ENST00000316997 — 16 exons

Exon	Start	End
ENSE00001417919	237798779	237798861
ENSE00001547537	237821071	237821254
ENSE00001553242	237820175	237820351
ENSE00001731498	237841839	237842805
ENSE00003515352	237816993	237818596
ENSE00003522973	237834278	237834423
ENSE00003533278	237827433	237827503
ENSE00003566579	237823440	237823554
ENSE00003580848	237833997	237834142
ENSE00003611478	237821743	237821827
ENSE00003626473	237821346	237821368
ENSE00003626621	237824291	237824419
ENSE00003633111	237813592	237813682
ENSE00003680675	237818901	237818959
ENSE00003681240	237829217	237829502
ENSE00003690865	237827250	237827329

Expression profiles

Bgee: expression breadth ubiquitous, 130 present calls, max score 86.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0906 / max 57.2878, expressed in 14 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26299	0.0764	14
26298	0.0142	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.90	gold quality
right testis	UBERON:0004534	82.22	gold quality
testis	UBERON:0000473	81.39	gold quality
left testis	UBERON:0004533	80.25	gold quality
thymus	UBERON:0002370	72.22	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	66.98	gold quality
monocyte	CL:0000576	66.94	gold quality
calcaneal tendon	UBERON:0003701	66.71	gold quality
bone marrow	UBERON:0002371	65.94	gold quality
leukocyte	CL:0000738	65.76	gold quality
quadriceps femoris	UBERON:0001377	65.49	gold quality
cerebellar vermis	UBERON:0004720	64.61	gold quality
cortical plate	UBERON:0005343	64.31	gold quality
tibial artery	UBERON:0007610	63.91	gold quality
popliteal artery	UBERON:0002250	63.88	gold quality
thoracic aorta	UBERON:0001515	63.82	gold quality
ascending aorta	UBERON:0001496	63.76	gold quality
mucosa of stomach	UBERON:0001199	63.61	gold quality
bone marrow cell	CL:0002092	63.38	gold quality
descending thoracic aorta	UBERON:0002345	63.35	gold quality
right coronary artery	UBERON:0001625	63.12	gold quality
subcutaneous adipose tissue	UBERON:0002190	62.96	gold quality
metanephros cortex	UBERON:0010533	62.39	gold quality
right lung	UBERON:0002167	61.93	gold quality
adipose tissue	UBERON:0001013	61.56	gold quality
upper lobe of left lung	UBERON:0008952	61.16	gold quality
left coronary artery	UBERON:0001626	60.93	gold quality
myometrium	UBERON:0001296	60.61	gold quality
smooth muscle tissue	UBERON:0001135	60.14	gold quality
omental fat pad	UBERON:0010414	59.92	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

81 targeting RBM44, 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-656-3P	100.00	72.15	2788
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-373-3P	99.84	70.68	1668

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rbm44	ENSMUSG00000070732
rattus_norvegicus	Rbm44	ENSRNOG00000024878

Protein

Protein identifiers

RNA-binding protein 44 — Q6ZP01 (reviewed: Q6ZP01)

Alternative names: RNA-binding motif protein 44

All UniProt accessions (1): Q6ZP01

UniProt curated annotations — full annotation on UniProt →

Function. Component of intercellular bridges during meiosis. Intercellular bridges are evolutionarily conserved structures that connect differentiating germ cells. Not required for fertility.

Subunit / interactions. Homodimer. Interacts with TEX14.

Subcellular location. Cytoplasm.

RefSeq proteins (1): NP_001073973* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR056870	TTC3/DZIP3/RBM44-like_helical	Domain

Pfam: PF00076, PF24905

UniProt features (18 total): region of interest 5, compositionally biased region 4, modified residue 4, sequence variant 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZP01-F1	45.58	0.06

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 (4): 388, 391, 546, 726

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_RNA_SPLICING, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_INTERCELLULAR_BRIDGE, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_PROTEIN_HOMODIMERIZATION_ACTIVITY, GOMF_MRNA_BINDING, GOMF_MRNA_3_UTR_BINDING, GOBP_MRNA_PROCESSING, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_12H_UP, HMGA1_TARGET_GENES

GO Biological Process (1): mRNA splicing, via spliceosome (GO:0000398)

GO Molecular Function (4): mRNA 3’-UTR binding (GO:0003730), protein homodimerization activity (GO:0042803), nucleic acid binding (GO:0003676), RNA binding (GO:0003723)

GO Cellular Component (3): cytoplasm (GO:0005737), intercellular bridge (GO:0045171), catalytic step 2 spliceosome (GO:0071013)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA binding	1
identical protein binding	1
protein dimerization activity	1
binding	1
nucleic acid binding	1
intracellular anatomical structure	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1

Protein interactions and networks

STRING

378 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM44	TEX14	Q8IWB6	757
RBM44	CEP55	Q53EZ4	553
RBM44	SRFBP1	Q8NEF9	520
RBM44	ASMTL	O95671	518
RBM44	C6orf52	Q5T4I8	507
RBM44	RAMP1	O60894	493
RBM44	TSN	Q15631	462
RBM44	NANOS2	P60321	460
RBM44	FAM181A	Q8N9Y4	443
RBM44	CCDC116	Q8IYX3	437
RBM44	NANOS3	P60323	437
RBM44	DAZL	Q92904	433
RBM44	LRRFIP1	Q32MZ4	433
RBM44	KIAA1210	Q9ULL0	402
RBM44	TIPE2	Q6P589	383

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RBM44	NPM1	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (3): RBM44 (Proximity Label-MS), RBM44 (Protein-RNA), RBM44 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WRU1, A0JNH1, A2RUB1, A6QNQ6, B0S6S9, B1WC58, D3Z987, D3ZJ47, E1BC15, O60673, P28358, P28359, P56716, P70347, Q0P5X5, Q0VAV2, Q0VBV7, Q15468, Q2M2Z5, Q3UXL4, Q3V089, Q49A88, Q569L8, Q5BQN8, Q5CZC0, Q5QGS0, Q5T1N1, Q5VWN6, Q60988, Q61493, Q62924, Q6ZP01, Q6ZU52, Q6ZVD7, Q80U59, Q80WQ8, Q86WS4, Q86YC2, Q8CB14, Q8IUR6

Diamond homologs: D3Z987, E1BC15, Q3V089, Q6ZP01

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	123
Likely benign	16
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2576 predictions. Top by Δscore:

Variant	Effect	Δscore
2:237813590:A:AG	acceptor_gain	1.0000
2:237813591:G:GG	acceptor_gain	1.0000
2:237813591:GATT:G	acceptor_gain	1.0000
2:237820287:A:G	donor_gain	1.0000
2:237820338:G:GT	donor_gain	1.0000
2:237820338:G:T	donor_gain	1.0000
2:237820342:GAT:G	donor_gain	1.0000
2:237821828:G:GG	donor_gain	1.0000
2:237823431:A:AG	acceptor_gain	1.0000
2:237823551:AAAG:A	donor_loss	1.0000
2:237823552:AAGG:A	donor_loss	1.0000
2:237823553:AGGTT:A	donor_loss	1.0000
2:237823555:G:GC	donor_loss	1.0000
2:237824416:GGAG:G	donor_gain	1.0000
2:237824417:GAGG:G	donor_gain	1.0000
2:237833993:TTAG:T	acceptor_loss	1.0000
2:237833995:A:AG	acceptor_gain	1.0000
2:237833995:AG:A	acceptor_gain	1.0000
2:237833996:G:A	acceptor_gain	1.0000
2:237833996:G:GG	acceptor_gain	1.0000
2:237833996:GGGT:G	acceptor_gain	1.0000
2:237834139:GCAG:G	donor_gain	1.0000
2:237834140:CAGGT:C	donor_loss	1.0000
2:237834141:AGGTA:A	donor_loss	1.0000
2:237834143:G:C	donor_loss	1.0000
2:237834144:T:A	donor_loss	1.0000
2:237834273:CATA:C	acceptor_loss	1.0000
2:237834274:ATAG:A	acceptor_loss	1.0000
2:237834275:T:G	acceptor_gain	1.0000
2:237834275:TA:T	acceptor_loss	1.0000

AlphaMissense

7015 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:237829261:C:A	A883D	0.986
2:237827440:T:C	L847S	0.985
2:237827452:T:C	F851S	0.984
2:237827451:T:C	F851L	0.976
2:237827453:C:A	F851L	0.976
2:237827453:C:G	F851L	0.976
2:237834090:A:C	S995R	0.976
2:237834092:C:A	S995R	0.976
2:237834092:C:G	S995R	0.976
2:237834115:T:C	L1003P	0.976
2:237829222:C:A	A870E	0.974
2:237834294:G:C	A1018P	0.973
2:237827301:T:A	V835D	0.971
2:237834298:T:C	L1019P	0.969
2:237818339:T:C	F475L	0.958
2:237818341:T:A	F475L	0.958
2:237818341:T:G	F475L	0.958
2:237829221:G:C	A870P	0.958
2:237820254:G:C	A607P	0.956
2:237834298:T:A	L1019H	0.956
2:237829228:T:A	L872H	0.954
2:237820267:T:C	L611P	0.953
2:237829228:T:C	L872P	0.949
2:237817487:A:C	S191R	0.948
2:237817489:T:A	S191R	0.948
2:237817489:T:G	S191R	0.948
2:237834115:T:A	L1003Q	0.947
2:237827310:T:A	L838H	0.946
2:237827461:A:C	Y854S	0.945
2:237829309:T:A	V899E	0.943

dbSNP variants (sampled 300 via entrez): RS1000020053 (2:237803485 A>T), RS1000046445 (2:237823772 ATTC>A), RS1000122494 (2:237840064 C>A,G,T), RS1000122606 (2:237833594 A>G), RS1000136905 (2:237796972 T>C), RS1000211012 (2:237837121 ACTC>A), RS1000313562 (2:237836737 G>A), RS1000426723 (2:237816368 C>T), RS1000445132 (2:237829788 A>G), RS1000473507 (2:237837446 A>T), RS1000567773 (2:237798728 G>A,C), RS1000568403 (2:237811803 C>A), RS1000635 (2:237826472 C>T), RS1000636 (2:237826693 G>A,T), RS1000774895 (2:237831410 A>G)

Disease associations

OMIM: gene MIM:621038 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004523_9	Resting metabolic rate	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008004	resting metabolic rate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol S	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Asbestos, Serpentine	decreases methylation	1

Clinical trials (associated diseases)

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