SRRM3

Summary

SRRM3 (serine/arginine repetitive matrix 3, HGNC:26729) is a protein-coding gene on chromosome 7q11.23, encoding Serine/arginine repetitive matrix protein 3 (A6NNA2). May play a role in regulating breast cancer cell invasiveness.

Predicted to enable mRNA binding activity. Predicted to be located in nucleus.

Source: NCBI Gene 222183 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 89 total
• MANE Select transcript: NM_001110199

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26729
Approved symbol	SRRM3
Name	serine/arginine repetitive matrix 3
Location	7q11.23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37078
Ensembl gene	ENSG00000177679
Ensembl biotype	protein_coding
Entrez	222183

Gene structure

Transcript identifiers

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

ENST00000464752, ENST00000479284, ENST00000479294, ENST00000611745, ENST00000612155

RefSeq mRNA: 2 — MANE Select: NM_001110199 NM_001110199, NM_001291831

Canonical transcript exons

ENST00000611745 — 15 exons

Exon	Start	End
ENSE00003712827	76282964	76283101
ENSE00003714040	76261546	76261581
ENSE00003718058	76235028	76235299
ENSE00003721529	76281441	76281802
ENSE00003724521	76285615	76287287
ENSE00003727848	76260117	76260197
ENSE00003729470	76267258	76267435
ENSE00003730600	76201896	76202067
ENSE00003734860	76259906	76260034
ENSE00003740449	76260874	76260903
ENSE00003744195	76261352	76261414
ENSE00003744529	76264765	76264815
ENSE00003744666	76248188	76248289
ENSE00003750512	76282648	76282872
ENSE00003753347	76265364	76265468

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 99.41.

FANTOM5 (CAGE): breadth broad, TPM avg 6.5437 / max 364.6760, expressed in 891 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
79146	3.1833	208
79155	2.7378	736
204496	0.3635	137
79152	0.0989	43
79145	0.0663	42
204495	0.0494	29
79147	0.0163	6
79148	0.0101	5
79149	0.0093	5
79150	0.0089	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	99.41	gold quality
cerebellar cortex	UBERON:0002129	99.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.35	gold quality
cerebellum	UBERON:0002037	98.02	gold quality
right frontal lobe	UBERON:0002810	95.83	gold quality
nucleus accumbens	UBERON:0001882	95.09	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.81	gold quality
putamen	UBERON:0001874	94.70	gold quality
caudate nucleus	UBERON:0001873	93.68	gold quality
anterior cingulate cortex	UBERON:0009835	93.49	gold quality
hypothalamus	UBERON:0001898	92.91	gold quality
cerebellar vermis	UBERON:0004720	92.81	gold quality
lower esophagus mucosa	UBERON:0035834	91.75	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.19	gold quality
left adrenal gland cortex	UBERON:0035825	90.04	gold quality
pituitary gland	UBERON:0000007	89.26	gold quality
amygdala	UBERON:0001876	89.12	gold quality
left adrenal gland	UBERON:0001234	89.09	gold quality
brain	UBERON:0000955	88.92	gold quality
right adrenal gland	UBERON:0001233	88.79	gold quality
adrenal cortex	UBERON:0001235	88.74	gold quality
adenohypophysis	UBERON:0002196	88.73	gold quality
right adrenal gland cortex	UBERON:0035827	88.58	gold quality
forebrain	UBERON:0001890	88.21	gold quality
neocortex	UBERON:0001950	87.99	gold quality
frontal cortex	UBERON:0001870	87.35	gold quality
apex of heart	UBERON:0002098	86.92	gold quality
cerebral cortex	UBERON:0000956	86.69	gold quality
adrenal gland	UBERON:0002369	86.24	gold quality
prefrontal cortex	UBERON:0000451	86.02	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	15.92
E-ANND-3	no	3.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting SRRM3, 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-4267	99.96	66.53	2368
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-3124-3P	98.87	68.95	2123
HSA-MIR-2355-5P	98.83	65.51	1589
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-5088-3P	98.29	66.63	1310
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-6762-5P	96.55	64.62	972
HSA-MIR-4264	96.35	64.76	1480
HSA-MIR-9900	96.06	65.48	557
HSA-MIR-4697-5P	95.38	61.72	457

Literature-anchored findings (GeneRIF, showing 2)

• RNA Splicing Factors SRRM3 and SRRM4 Distinguish Molecular Phenotypes of Castration-Resistant Neuroendocrine Prostate Cancer. (PMID:34312180)
• Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision. (PMID:35858306)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Srrm3	ENSMUSG00000039860
rattus_norvegicus	Srrm3	ENSRNOG00000001439

Protein

Protein identifiers

Serine/arginine repetitive matrix protein 3 — A6NNA2 (reviewed: A6NNA2)

All UniProt accessions (2): A0A087WXA3, A0A087X0W5

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in regulating breast cancer cell invasiveness. May be involved in RYBP-mediated breast cancer progression.

Tissue specificity. Expressed in breast cancer cell lines.

Similarity. Belongs to the CWC21 family.

RefSeq proteins (2): NP_001103669, NP_001278760 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013170	mRNA_splic_Cwf21_dom	Domain
IPR029360	SRRM_C	Domain
IPR047489	SRRM3_cwf21	Domain
IPR052109	SRRM_Domain-Containing	Family

Pfam: PF08312, PF15230

UniProt features (21 total): compositionally biased region 16, region of interest 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NNA2-F1	49.95	0.07

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 64 (showing top): CAGCTG_AP4_Q5, CATRRAGC_UNKNOWN, chr7q11, WHN_B, AP2_Q6_01, AP2GAMMA_01, AP4_01, GOMF_MRNA_BINDING, GGGGCCC_MIR296, MIKKELSEN_ES_ICP_WITH_H3K4ME3, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CBX5_TARGET_GENES, CHAF1B_TARGET_GENES, CIITA_TARGET_GENES, DROSHA_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): mRNA binding (GO:0003729)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1688 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SRRM3	SRRM1	Q8IYB3	503
SRRM3	RNPS1	Q15287	478
SRRM3	SRSF11	Q05519	459
SRRM3	FKBP6	O75344	416
SRRM3	U2AF1	Q01081	391
SRRM3	ISLR2	Q6UXK2	367
SRRM3	FAM117B	Q6P1L5	357
SRRM3	CDCP2	Q5VXM1	356
SRRM3	UEVLD	Q8IX04	353
SRRM3	RCC1L	Q96I51	350
SRRM3	CDC5L	Q99459	348
SRRM3	EFTUD2	Q15029	348
SRRM3	GAPVD1	Q14C86	343
SRRM3	SNRPA1	P09661	340
SRRM3	PRPF8	Q6P2Q9	340

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A4D2P6, A6NNA2, A7MD48, A8IHN8, C9JLR9, G3V9M2, O00287, O95644, P04198, P12755, P18444, P49796, P49797, P51608, P55199, Q00566, Q08DA0, Q0PHV7, Q13387, Q1W6H9, Q29RS4, Q3UPL5, Q3YEC7, Q4QQU1, Q4VA45, Q5XKK7, Q61976, Q6NV74, Q6R891, Q7Z6J2, Q80WV7, Q80YR4, Q86UK7, Q8BKA3, Q8N554, Q8R149, Q8R4T5, Q8TF61, Q8VCG9, Q95LG8

Diamond homologs: A6NNA2, Q5AP89, Q6C0M9, Q80WV7, Q8BTI8, Q9U213, Q9UQ35, P0CM94, P0CM95, Q03375, Q4IB70, Q4P0G6, Q6BWB8, Q6FRM6, Q751G9, Q7RYH7, A7MD48, P0CB65, Q8BKA3, O14161, Q4WDD0, Q6CVR3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	82
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2265 predictions. Top by Δscore:

Variant	Effect	Δscore
7:76235297:GGG:G	donor_gain	1.0000
7:76235298:GGG:G	donor_gain	1.0000
7:76248182:CTGCA:C	acceptor_loss	1.0000
7:76248183:TGCA:T	acceptor_loss	1.0000
7:76248184:GCAG:G	acceptor_loss	1.0000
7:76248185:CAG:C	acceptor_loss	1.0000
7:76248186:A:G	acceptor_loss	1.0000
7:76248252:G:GT	donor_gain	1.0000
7:76248266:G:GT	donor_gain	1.0000
7:76248290:G:GG	donor_gain	1.0000
7:76260113:CCA:C	acceptor_loss	1.0000
7:76260114:CA:C	acceptor_loss	1.0000
7:76260115:A:AC	acceptor_loss	1.0000
7:76260194:GCCG:G	donor_gain	1.0000
7:76260858:T:A	acceptor_gain	1.0000
7:76260859:G:A	acceptor_gain	1.0000
7:76260863:T:G	acceptor_gain	1.0000
7:76261343:T:TA	acceptor_gain	1.0000
7:76261347:CACAG:C	acceptor_loss	1.0000
7:76261350:A:AG	acceptor_gain	1.0000
7:76261350:AGCT:A	acceptor_gain	1.0000
7:76261350:AGCTG:A	acceptor_loss	1.0000
7:76261351:G:GA	acceptor_gain	1.0000
7:76261351:GCT:G	acceptor_gain	1.0000
7:76261351:GCTG:G	acceptor_gain	1.0000
7:76261351:GCTGT:G	acceptor_gain	1.0000
7:76261411:ACAGG:A	donor_loss	1.0000
7:76261412:CAGG:C	donor_loss	1.0000
7:76261413:AGGTA:A	donor_loss	1.0000
7:76261414:GGTAC:G	donor_loss	1.0000

AlphaMissense

4201 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000103910 (7:76220092 C>G,T), RS1000136274 (7:76261183 C>A,G,T), RS1000159894 (7:76228999 C>A,T), RS1000201692 (7:76203631 C>A), RS1000254084 (7:76203865 G>A,C), RS1000345802 (7:76238927 G>A), RS1000399567 (7:76238590 G>A,C), RS1000471970 (7:76231909 G>A), RS1000501241 (7:76287741 T>C), RS1000507955 (7:76242951 G>A), RS1000535995 (7:76202193 G>A), RS1000559366 (7:76219838 A>G), RS1000574937 (7:76287511 G>A,C), RS1000697054 (7:76280989 C>A), RS1000707756 (7:76273907 C>T)

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

3 associations (top):

Study	Trait	p-value
GCST008529_11	Tea consumption	1.000000e-09
GCST009447_12	Parental longevity (father’s age at death)	5.000000e-08
GCST010243_56	Apolipoprotein B levels	2.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0010091	tea consumption measurement
EFO:0007796	parental longevity
EFO:0004615	apolipoprotein B measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, affects cotreatment, increases expression	2
Benzo(a)pyrene	affects methylation, increases expression, increases methylation	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Valproic Acid	affects expression, increases methylation	2
aristolochic acid I	decreases expression	1
OTX015	decreases expression	1
bisphenol F	affects cotreatment, increases expression	1
mivebresib	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
2-palmitoylglycerol	increases expression	1
bisphenol S	increases methylation	1
(+)-JQ1 compound	decreases expression	1
Arsenic	affects methylation	1
Calcitriol	increases expression, affects cotreatment	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Testosterone	affects cotreatment, increases expression	1
Triclosan	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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