HNRNPA1L3

Summary

HNRNPA1L3 (heterogeneous nuclear ribonucleoprotein A1 like 3, HGNC:48778) is a protein-coding gene on chromosome 16q12.1, encoding Heterogeneous nuclear ribonucleoprotein A1-like 3 (A0A2R8Y4L2).

Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of catalytic step 2 spliceosome.

Source: NCBI Gene 642659 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001396241

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48778
Approved symbol	HNRNPA1L3
Name	heterogeneous nuclear ribonucleoprotein A1 like 3
Location	16q12.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000224578
Ensembl biotype	protein_coding
Entrez	642659

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000565308, ENST00000698152

RefSeq mRNA: 1 — MANE Select: NM_001396241 NM_001396241

CCDS: CCDS92159

Canonical transcript exons

ENST00000698152 — 1 exons

Exon	Start	End
ENSE00003972857	51645757	51647079

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 88.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.7396 / max 32.5324, expressed in 1048 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154046	1.7396	1048

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	88.61	gold quality
cortical plate	UBERON:0005343	87.56	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.91	gold quality
ventricular zone	UBERON:0003053	82.27	gold quality
bone marrow cell	CL:0002092	81.95	gold quality
bone marrow	UBERON:0002371	79.98	gold quality
ovary	UBERON:0000992	78.64	gold quality
left ovary	UBERON:0002119	78.00	gold quality
vermiform appendix	UBERON:0001154	77.68	gold quality
duodenum	UBERON:0002114	77.32	gold quality
tonsil	UBERON:0002372	77.13	gold quality
placenta	UBERON:0001987	76.31	gold quality
right ovary	UBERON:0002118	75.29	gold quality
stromal cell of endometrium	CL:0002255	74.14	gold quality
leukocyte	CL:0000738	73.61	gold quality
monocyte	CL:0000576	73.59	gold quality
endometrium	UBERON:0001295	72.90	gold quality
islet of Langerhans	UBERON:0000006	72.45	gold quality
urinary bladder	UBERON:0001255	72.41	gold quality
uterine cervix	UBERON:0000002	72.26	gold quality
lymph node	UBERON:0000029	71.99	gold quality
skeletal muscle tissue	UBERON:0001134	71.69	gold quality
granulocyte	CL:0000094	71.67	gold quality
ectocervix	UBERON:0012249	71.66	gold quality
body of uterus	UBERON:0009853	71.38	gold quality
myometrium	UBERON:0001296	71.27	gold quality
mucosa of transverse colon	UBERON:0004991	70.90	gold quality
mucosa of stomach	UBERON:0001199	70.88	gold quality
pancreas	UBERON:0001264	70.79	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-124472	yes	1241.77
E-MTAB-6701	yes	544.92
E-HCAD-10	yes	35.63
E-ANND-3	yes	19.25
E-GEOD-125970	yes	14.63
E-GEOD-135922	yes	10.75
E-CURD-79	no	582.59
E-MTAB-8221	no	305.12
E-GEOD-93593	no	8.60
E-MTAB-5061	no	3.87

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio	hnrnpa1b	ENSDARG00000036675

Paralogs (36): DAZAP1 (ENSG00000071626), CIRBP (ENSG00000099622), RBM23 (ENSG00000100461), RBM3 (ENSG00000102317), NCL (ENSG00000115053), TIA1 (ENSG00000116001), HNRNPA2B1 (ENSG00000122566), RBM19 (ENSG00000122965), RBM39 (ENSG00000131051), MSI1 (ENSG00000135097), HNRNPA1 (ENSG00000135486), HNRNPD (ENSG00000138668), HNRNPA1L2 (ENSG00000139675), RBMX (ENSG00000147274), A1CF (ENSG00000148584), TIAL1 (ENSG00000151923), RBM46 (ENSG00000151962), HNRNPDL (ENSG00000152795), MSI2 (ENSG00000153944), RBM47 (ENSG00000163694), RBMY1F (ENSG00000169800), HNRNPA3 (ENSG00000170144), RBMXL2 (ENSG00000170748), RBM4B (ENSG00000173914), RBM4 (ENSG00000173933), RBMXL3 (ENSG00000175718), HNRNPA0 (ENSG00000177733), TRNAU1AP (ENSG00000180098), HNRNPAB (ENSG00000197451), RBMXL1 (ENSG00000213516), RBMY1J (ENSG00000226941), RBMY1A1 (ENSG00000234414), RBMY1E (ENSG00000242389), RBMY1B (ENSG00000242875), RBMY1D (ENSG00000244395), DND1 (ENSG00000256453)

Protein

Protein identifiers

Heterogeneous nuclear ribonucleoprotein A1-like 3 — A0A2R8Y4L2 (reviewed: A0A2R8Y4L2)

Alternative names: Heterogeneous nuclear ribonucleoprotein A1 pseudogene 48

All UniProt accessions (1): A0A2R8Y4L2

RefSeq proteins (1): NP_001383170* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR021662	HnRNPA1/A2_C	Domain
IPR034516	hnRNPA1/3_RRM2	Domain
IPR034845	hnRNPA1_RRM1	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily

Pfam: PF00076, PF11627

UniProt features (7 total): domain 2, region of interest 2, compositionally biased region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A2R8Y4L2-F1	73.41	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): GOBP_RNA_SPLICING, GOCC_CATALYTIC_STEP_2_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOMF_MRNA_BINDING, GOMF_MRNA_3_UTR_BINDING, GOBP_MRNA_PROCESSING, MENON_FETAL_KIDNEY_0_CAP_MESENCHYME_CELLS, HU_FETAL_RETINA_RPC, DESCARTES_FETAL_LUNG_CSH1_CSH2_POSITIVE_CELLS, GOCC_NUCLEAR_PROTEIN_CONTAINING_COMPLEX, BDP1_TARGET_GENES, HE_LIM_SUN_FETAL_LUNG_C0_ACTC_POS_SMC_CELL, HE_LIM_SUN_FETAL_LUNG_C0_EARLY_FIBROBLAST, HE_LIM_SUN_FETAL_LUNG_C0_EARLY_MESOTHELIAL_CELL

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

GO Molecular Function (3): mRNA 3’-UTR binding (GO:0003730), nucleic acid binding (GO:0003676), RNA binding (GO:0003723)

GO Cellular Component (2): catalytic step 2 spliceosome (GO:0071013), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	1
mRNA processing	1
mRNA binding	1
binding	1
nucleic acid binding	1
Prp19 complex	1
spliceosomal complex	1
U5 snRNP	1
catalytic complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1416 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HNRNPA1L3	CHRNA1	P02708	349
HNRNPA1L3	PLD5	Q8N7P1	349
HNRNPA1L3	PNPLA8	Q9NP80	348
HNRNPA1L3	RAVER1	Q8IY67	348
HNRNPA1L3	MATR3	P43243	340
HNRNPA1L3	PRSS21	Q9Y6M0	335
HNRNPA1L3	FUNDC2	Q9BWH2	335
HNRNPA1L3	RPL10A	P52859	335
HNRNPA1L3	DOCK1	Q14185	331
HNRNPA1L3	MAP3K7CL	P57077	306
HNRNPA1L3	RAB28	P51157	305
HNRNPA1L3	PTTG1	O95997	291
HNRNPA1L3	CSMD3	Q7Z407	285
HNRNPA1L3	TACSTD2	P09758	284
HNRNPA1L3	RAB30	Q15771	267

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0A0LLY1, A0A2R8Y4L2, A5A6H4, O89086, O93235, P04256, P09651, P09867, P10979, P17130, P21522, P27484, P49310, P49311, P49312, P51968, P51989, P51991, P51992, P60824, P60825, P60826, P98179, Q03250, Q03251, Q03878, Q05966, Q13151, Q14011, Q28521, Q28IQ9, Q2HJ60, Q32P51, Q38896, Q41188, Q43472, Q5RF83, Q61B10, Q6URK4, Q8BG05

Diamond homologs: A0A0A0LLY1, A0A0D1C8Z4, A0A2R8Y4L2, A5A6H4, A5A6M3, A7VJC2, D4AE41, O22703, O75526, O88569, O89086, O93235, P04256, P09651, P09867, P10979, P17130, P19682, P19683, P19684, P22626, P28644, P38159, P39697, P41891, P49310, P49311, P49312, P49313, P49314, P51968, P51989, P51990, P51991, P51992, P60824, P60825, P60826, P84586, P98179

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1002130810 (16:51644353 G>A), RS1002445447 (16:51643828 C>T), RS1002738459 (16:51645486 T>G), RS1006227606 (16:51644265 T>C), RS1006302959 (16:51644121 G>A,C), RS1007530833 (16:51647526 C>T), RS1008061135 (16:51647258 T>A,C), RS1009030653 (16:51645816 T>C), RS1009364341 (16:51644692 A>G), RS1010374625 (16:51644686 T>C,G), RS1011384297 (16:51647151 A>C,G), RS1011500941 (16:51645552 T>A,C), RS1013232535 (16:51645309 T>C), RS1013258974 (16:51645079 G>A), RS1013341196 (16:51646016 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
bisphenol A	decreases expression	1
ochratoxin A	affects cotreatment, decreases expression	1
Citrinin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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