SRBD1

gene
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Also known as FLJ10379

Summary

SRBD1 (S1 RNA binding domain 1, HGNC:25521) is a protein-coding gene on chromosome 2p21, encoding S1 RNA-binding domain-containing protein 1 (Q8N5C6). DNA- and histone-binding protein that localizes to the central axes of mitotic chromosomes. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

Predicted to enable mRNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation.

Source: NCBI Gene 55133 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 195 total
  • Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
  • MANE Select transcript: NM_018079

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25521
Approved symbolSRBD1
NameS1 RNA binding domain 1
Location2p21
Locus typegene with protein product
StatusApproved
AliasesFLJ10379
Ensembl geneENSG00000068784
Ensembl biotypeprotein_coding
Entrez55133

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000263736, ENST00000461805, ENST00000475073, ENST00000490133, ENST00000493649, ENST00000922966

RefSeq mRNA: 1 — MANE Select: NM_018079 NM_018079

CCDS: CCDS1823

Canonical transcript exons

ENST00000263736 — 21 exons

ExonStartEnd
ENSE000007509034547699345477075
ENSE000008097854557320745573342
ENSE000010057924560190345602083
ENSE000011688154538868045389599
ENSE000011688254557462745574723
ENSE000011694034559944945599835
ENSE000013460894557987545580013
ENSE000013460934558169345581810
ENSE000013460954558560845585774
ENSE000013461104561121945611267
ENSE000034857724560536245605441
ENSE000034880674555362345553730
ENSE000034918964541311445413293
ENSE000034957234539294545393129
ENSE000035440554554752245547612
ENSE000035538514548824045488331
ENSE000036252404541978845419894
ENSE000036389274554673245546839
ENSE000036575054556265345562756
ENSE000036718174541836545418541
ENSE000036945164555112545551282

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 89.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.8930 / max 234.2335, expressed in 1778 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
2818011.72251773
281750.8981263
281760.2724124

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.56gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.38gold quality
monocyteCL:000057686.96gold quality
mononuclear cellCL:000084286.62gold quality
leukocyteCL:000073886.33gold quality
calcaneal tendonUBERON:000370186.21gold quality
islet of LangerhansUBERON:000000684.57gold quality
ventricular zoneUBERON:000305384.52gold quality
corpus epididymisUBERON:000435983.32gold quality
rectumUBERON:000105281.27gold quality
ganglionic eminenceUBERON:000402380.72gold quality
bloodUBERON:000017880.46gold quality
tendonUBERON:000004380.23gold quality
pancreasUBERON:000126480.22gold quality
sural nerveUBERON:001548879.93gold quality
granulocyteCL:000009479.49gold quality
stromal cell of endometriumCL:000225579.38gold quality
adrenal tissueUBERON:001830378.96gold quality
body of pancreasUBERON:000115078.87gold quality
choroid plexus epitheliumUBERON:000391177.98silver quality
gall bladderUBERON:000211076.98gold quality
bone marrow cellCL:000209276.80gold quality
ectocervixUBERON:001224976.21gold quality
popliteal arteryUBERON:000225076.15gold quality
tibial arteryUBERON:000761076.15gold quality
right adrenal gland cortexUBERON:003582775.86gold quality
smooth muscle tissueUBERON:000113575.80gold quality
secondary oocyteCL:000065575.79gold quality
colonic epitheliumUBERON:000039775.73gold quality
caput epididymisUBERON:000435875.68gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

58 targeting SRBD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4533100.0069.482758
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3163100.0077.238605
HSA-MIR-548AW99.9972.573559
HSA-MIR-366299.9973.825684
HSA-MIR-511-3P99.9968.851467
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4482-3P99.9872.503147
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-651-3P99.9473.485177
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-367199.9073.043897
HSA-MIR-612499.8769.783551
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-469899.8471.414303
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-4694-3P99.7969.532640

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

  • Our genome-wide association study identified SRBD1 and ELOVL5 as new susceptibility genes for (normal tension glaucoma) NTG. (PMID:20363506)
  • Dogs and humans share a common susceptibility gene SRBD1 for glaucoma risk. (PMID:24040232)
  • rs3213787 and rs11884064 not associated with genetic susceptibility to normal-tension glaucoma in a Korean cohort (PMID:32569157)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriosrbd1ENSDARG00000079827
danio_reriosrbd1ENSDARG00000092855
mus_musculusSrbd1ENSMUSG00000024135
rattus_norvegicusSrbd1ENSRNOG00000014720
drosophila_melanogasterCG31156FBGN0051156
caenorhabditis_elegansZK973.1WBGENE00022830

Protein

Protein identifiers

S1 RNA-binding domain-containing protein 1Q8N5C6 (reviewed: Q8N5C6)

All UniProt accessions (1): Q8N5C6

UniProt curated annotations — full annotation on UniProt →

Function. DNA- and histone-binding protein that localizes to the central axes of mitotic chromosomes. Promotes chromosome segregation by facilitating TOP2A recruitment to mitotic chromosomes, thereby preventing anaphase failure. During prophase, safeguards the decatenation process to avoid the formation of difficult-to-resolve DNA structures, preventing chromosome missegregation. Also contributes to the regulation of nucleus pulposus cell senescence.

Subunit / interactions. Interacts with NBR1; this interaction clears SRBD1 through the autophagic-lysosomal pathway.

Subcellular location. Nucleus. Nucleolus. Cytoplasm. Chromosome.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N5C6-11yes
Q8N5C6-22

RefSeq proteins (1): NP_060549* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003029S1_domainDomain
IPR006641YqgF/RNaseH-like_domDomain
IPR010994RuvA_2-likeHomologous_superfamily
IPR012337RNaseH-like_sfHomologous_superfamily
IPR012340NA-bd_OB-foldHomologous_superfamily
IPR018974Tex-like_NDomain
IPR023319Tex-like_HTH_dom_sfHomologous_superfamily
IPR023323Tex-like_dom_sfHomologous_superfamily
IPR032639Tex_YqgFDomain
IPR037027YqgF/RNaseH-like_dom_sfHomologous_superfamily
IPR041692HHH_9Domain
IPR044146S1_TexDomain
IPR050437Ribos_protein_bS1-likeFamily
IPR055179Tex-like_central_regionDomain

Pfam: PF00575, PF09371, PF12836, PF16921, PF17674, PF22706

UniProt features (23 total): cross-link 8, sequence variant 3, sequence conflict 3, region of interest 2, modified residue 2, chain 1, domain 1, splice variant 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N5C6-F175.680.52

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 (10): 166, 167, 183, 185, 185, 955, 861, 964, 84, 134

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 105 (showing top): GOBP_TRANSLATION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, AACTTT_UNKNOWN, NUYTTEN_EZH2_TARGETS_DN, SCGGAAGY_ELK1_02, GOMF_MRNA_BINDING, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, ELK1_02, PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN, ATF5_TARGET_GENES, ELF2_TARGET_GENES, FOXE1_TARGET_GENES, HES2_TARGET_GENES, KAT5_TARGET_GENES, MAFG_TARGET_GENES

GO Biological Process (2): nucleobase-containing compound metabolic process (GO:0006139), translation (GO:0006412)

GO Molecular Function (4): mRNA binding (GO:0003729), structural constituent of ribosome (GO:0003735), nucleic acid binding (GO:0003676), RNA binding (GO:0003723)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
primary metabolic process1
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
RNA binding1
structural molecule activity1
ribosome1
binding1
nucleic acid binding1

Protein interactions and networks

STRING

1932 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SRBD1TMCO1Q9UM00613
SRBD1SIX1Q15475606
SRBD1ASB10Q8WXI3573
SRBD1ELOVL5Q9NYP7571
SRBD1MYOCQ99972549
SRBD1WDR36Q8NI36530
SRBD1SIX6O95475507
SRBD1ATOH7Q8N100505
SRBD1ZNF362Q5T0B9490
SRBD1ZNF276Q8N554490
SRBD1CAV2P51636474
SRBD1RRP15Q9Y3B9472
SRBD1GAS7O60861466
SRBD1FEZ2Q9UHY8462
SRBD1NAIF1Q69YI7448

IntAct

104 interactions, top by confidence:

ABTypeScore
SART3PRPF4psi-mi:“MI:0914”(association)0.730
ZC3HC1TPRpsi-mi:“MI:0914”(association)0.640
KPNA1TCERG1psi-mi:“MI:0914”(association)0.640
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
TRIM44ODAD3psi-mi:“MI:0914”(association)0.530
RRP8NVLpsi-mi:“MI:0914”(association)0.530
RPL18ARRP8psi-mi:“MI:0914”(association)0.530
ZBTB48ZBTB24psi-mi:“MI:0914”(association)0.530
ARIH1SPOPpsi-mi:“MI:0914”(association)0.530
SRBD1PPP3CCpsi-mi:“MI:0914”(association)0.530
RPS3ZNF316psi-mi:“MI:0914”(association)0.530
MAGEB2POLRMTpsi-mi:“MI:0914”(association)0.530
CCDC59GAPDHSpsi-mi:“MI:0914”(association)0.530
MYL6MYL6Bpsi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPL13RRP8psi-mi:“MI:0914”(association)0.530
H3C1SMCHD1psi-mi:“MI:2364”(proximity)0.410
SRBD1GAPDHSpsi-mi:“MI:0915”(physical association)0.400
Lyplal1PARP10psi-mi:“MI:0914”(association)0.350
Naa50WDR46psi-mi:“MI:0914”(association)0.350

BioGRID (150): SRBD1 (Affinity Capture-RNA), SRBD1 (Affinity Capture-MS), SRBD1 (Proximity Label-MS), SRBD1 (Proximity Label-MS), SRBD1 (Proximity Label-MS), SRBD1 (Affinity Capture-MS), SRBD1 (Affinity Capture-MS), SRBD1 (Affinity Capture-MS), SRBD1 (Affinity Capture-MS), SRBD1 (Affinity Capture-MS), SRBD1 (Synthetic Lethality), RCAN1 (Affinity Capture-MS), GSK3A (Affinity Capture-MS), SRBD1 (Affinity Capture-MS), SRBD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8J1M587, A2PYH4, A2RUV5, A8WK63, B2RR83, B3MMA5, B3P3W1, B4K5R2, B4MX21, B6DMK2, B8A4F4, D3Z4R1, F1NTD6, O09053, O13799, O14232, O18475, O48534, O60072, O75417, O93530, P46063, P51979, P53327, Q14BI7, Q1LXK4, Q2VPA6, Q3EBC8, Q3MHU3, Q3YK19, Q497V5, Q5D892, Q5N870, Q5R746, Q5RDI0, Q5RF63, Q5SXJ3, Q6AYJ1, Q6J5K9, Q7QCW2

Diamond homologs: A0LE14, A0Q0Q1, A0QYY6, A1WXU7, A2ZLC1, A3PNG0, A4WWP0, A5GF91, A6LSR0, A7IC03, A8IGA3, A8J637, A8LKE7, A9KNK6, B0K1D0, B0K9P4, B0T175, B2FN86, B2TJ61, B2V4H5, B3EAF2, B4SQR6, B5EI63, B6IVG3, B7JJ84, B8I2R5, B9KP47, B9M1G5, C6E2P5, O06000, O31489, P0AG67, P0AG68, P0AG69, P0AG70, P14128, P14129, P37985, P38494, P46836

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 131 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
SARS-CoV-1 modulates host translation machinery724.0×4e-07
Eukaryotic Translation Initiation620.6×8e-06
Cap-dependent Translation Initiation620.6×8e-06
Eukaryotic Translation Elongation618.6×1e-05
Peptide chain elongation1318.3×3e-11
Viral mRNA Translation1318.3×3e-11
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1318.1×3e-11
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S618.1×2e-05

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1421.8×2e-12
ribosomal small subunit biogenesis917.2×6e-07
translation1210.4×6e-07
regulation of alternative mRNA splicing, via spliceosome510.3×1e-02
negative regulation of translation69.9×3e-03
rRNA processing89.5×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance159
Likely benign11
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4367 predictions. Top by Δscore:

VariantEffectΔscore
2:45389595:AAAAT:Aacceptor_gain1.0000
2:45389596:AAAT:Aacceptor_gain1.0000
2:45389597:AAT:Aacceptor_gain1.0000
2:45389597:AATCT:Aacceptor_loss1.0000
2:45389598:AT:Aacceptor_gain1.0000
2:45389599:TCTG:Tacceptor_loss1.0000
2:45389600:C:CCacceptor_gain1.0000
2:45389600:C:CGacceptor_loss1.0000
2:45392940:TTTA:Tdonor_loss1.0000
2:45392941:TTA:Tdonor_loss1.0000
2:45392942:TA:Tdonor_loss1.0000
2:45392943:A:AGdonor_loss1.0000
2:45392944:C:Adonor_loss1.0000
2:45393125:AAAAC:Aacceptor_gain1.0000
2:45393126:AAAC:Aacceptor_gain1.0000
2:45393126:AAACC:Aacceptor_loss1.0000
2:45393127:AAC:Aacceptor_gain1.0000
2:45393127:AACCT:Aacceptor_loss1.0000
2:45393128:AC:Aacceptor_gain1.0000
2:45393129:CC:Cacceptor_gain1.0000
2:45393129:CCTG:Cacceptor_loss1.0000
2:45393130:C:CCacceptor_gain1.0000
2:45393130:C:CGacceptor_loss1.0000
2:45393131:T:Aacceptor_loss1.0000
2:45393134:A:Tacceptor_gain1.0000
2:45393135:G:GCacceptor_gain1.0000
2:45413109:CTTA:Cdonor_loss1.0000
2:45413111:TACC:Tdonor_loss1.0000
2:45413112:A:Tdonor_loss1.0000
2:45413113:CCT:Cdonor_gain1.0000

AlphaMissense

6549 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:45562740:C:GR441P1.000
2:45389332:A:GL989P0.999
2:45389500:C:TG933E0.999
2:45389521:A:TV926D0.999
2:45389527:C:TG924D0.999
2:45418491:C:GR736P0.999
2:45477060:C:GR661P0.999
2:45488244:A:CS654R0.999
2:45488244:A:TS654R0.999
2:45488246:T:GS654R0.999
2:45488298:A:CS636R0.999
2:45488298:A:TS636R0.999
2:45488300:T:GS636R0.999
2:45546819:C:TG596E0.999
2:45551178:C:TG541E0.999
2:45551179:C:GG541R0.999
2:45551179:C:TG541R0.999
2:45551226:A:GL525P0.999
2:45562719:A:GL448P0.999
2:45562741:G:TR441S0.999
2:45389374:A:TV975D0.998
2:45389464:A:GL945P0.998
2:45389491:A:TV936E0.998
2:45389501:C:GG933R0.998
2:45389501:C:TG933R0.998
2:45389502:A:CF932L0.998
2:45389502:A:TF932L0.998
2:45389504:A:GF932L0.998
2:45389533:A:GL922P0.998
2:45418403:G:CF765L0.998

dbSNP variants (sampled 300 via entrez): RS1000009040 (2:45425594 C>T), RS1000010518 (2:45422723 A>T), RS1000021574 (2:45567714 G>A), RS1000026370 (2:45427926 T>C), RS1000033028 (2:45569183 CTTT>C), RS1000047315 (2:45580610 C>G,T), RS1000048450 (2:45604078 A>C), RS1000055072 (2:45533213 C>T), RS1000072872 (2:45464810 G>C), RS1000095355 (2:45564284 A>C), RS1000120697 (2:45412659 T>A), RS1000125919 (2:45514248 T>C), RS1000130664 (2:45562158 CTTATT>C), RS1000144775 (2:45497613 T>A), RS1000147270 (2:45502648 G>A,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

7 associations (top):

StudyTraitp-value
GCST000645_1Glaucoma3.000000e-09
GCST002806_1Type 2 diabetes1.000000e-06
GCST002815_3Bipolar disorder (inflammation and infection response interaction)8.000000e-07
GCST002875_30Diisocyanate-induced asthma2.000000e-06
GCST004750_67Squamous cell lung carcinoma5.000000e-06
GCST009426_1Retinal arteriole-to-venule ratio7.000000e-07
GCST90014033_9Haemorrhoidal disease3.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007050HSV1 seropositivity
EFO:0006995response to diisocyanate
EFO:0010554retinal vasculature measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression3
GSK-J4decreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression1
potassium chromate(VI)decreases expression, affects cotreatment1
beta-methylcholineaffects expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
entinostatincreases expression1
(+)-JQ1 compounddecreases expression1
Sunitinibincreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Cadmiumincreases abundance, increases expression1
Caffeineaffects phosphorylation1
Cisplatindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ribonucleotidesaffects binding1
Tretinoinincreases expression1
Urethanedecreases expression1
Valproic Acidaffects expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporineincreases expression1
Cadmium Chlorideincreases expression, increases abundance1
Particulate Matterincreases abundance, decreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): glaucoma, hemorrhoid