Human Gene SRBD1 (uc002rus.3) Description and Page Index
  Description: Homo sapiens S1 RNA binding domain 1 (SRBD1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:45,615,819-45,838,433 Size: 222,615 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr2:45,616,449-45,832,580 Size: 216,132 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:45,615,819-45,838,433)mRNA (may differ from genome)Protein (995 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SRBD1_HUMAN
DESCRIPTION: RecName: Full=S1 RNA-binding domain-containing protein 1;
SIMILARITY: Contains 1 S1 motif domain.
SEQUENCE CAUTION: Sequence=AAY14821.1; Type=Erroneous gene model prediction;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SRBD1
CDC HuGE Published Literature: SRBD1
Positive Disease Associations: Alcoholism , Body Height , Cardiovascular Diseases
Related Studies:
  1. Alcoholism
    , , . [PubMed 0]
  2. Body Height
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Cardiovascular Diseases
    Akira Meguro et al. Ophthalmology 2010, Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility., Ophthalmology. [PubMed 20363506]
    Our genome-wide association study identified SRBD1 and ELOVL5 as new susceptibility genes for NTG. Because SRBD1 and ELOVL5 are reportedly involved in the induction of cell growth inhibition or apoptosis, the regulation of SRBD1 and ELOVL5 cascades may play an important physiologic role in the risk of NTG development.
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-  MalaCards Disease Associations
  MalaCards Gene Search: SRBD1
Diseases sorted by gene-association score: glaucoma, normal tension (2), glaucoma 1, open angle, e (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.65 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 115.78 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -28.8076-0.379 Picture PostScript Text
3' UTR -124.36630-0.197 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR003029 - Rbsml_prot_S1_RNA-bd_dom
IPR022967 - RNA-binding_domain_S1
IPR023323 - Tex-like_dom
IPR023319 - Tex-like_HTH_dom
IPR018974 - Tex-like_N
IPR023097 - Tex_RuvX-like_dom
IPR006641 - YqgF/RNaseH-like_dom

Pfam Domains:
PF00575 - S1 RNA binding domain
PF09371 - Tex-like protein N-terminal domain
PF12836 - Helix-hairpin-helix motif
PF14635 - Helix-hairpin-helix motif
PF16921 - Tex protein YqgF-like domain

SCOP Domains:
50249 - Nucleic acid-binding proteins

ModBase Predicted Comparative 3D Structure on Q8N5C6
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  EnsemblFlyBaseWormBase 
  Protein SequenceProtein SequenceProtein Sequence 
  AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Biological Process:
GO:0006139 nucleobase-containing compound metabolic process


-  Descriptions from all associated GenBank mRNAs
  LF210947 - JP 2014500723-A/18450: Polycomb-Associated Non-Coding RNAs.
BC032538 - Homo sapiens S1 RNA binding domain 1, mRNA (cDNA clone MGC:45074 IMAGE:5528417), complete cds.
AK056536 - Homo sapiens cDNA FLJ31974 fis, clone NT2RP7008167, weakly similar to 85.1 KDA PROTEIN IN GREB-FEOA INTERGENIC REGION.
AK001241 - Homo sapiens cDNA FLJ10379 fis, clone NT2RM2002014.
AK301122 - Homo sapiens cDNA FLJ57207 complete cds.
AK316222 - Homo sapiens cDNA, FLJ79121 complete cds, highly similar to Homo sapiens S1 RNA binding domain 1 (SRBD1).
JF432253 - Synthetic construct Homo sapiens clone IMAGE:100073423 S1 RNA binding domain 1 (SRBD1) gene, encodes complete protein.
KJ902773 - Synthetic construct Homo sapiens clone ccsbBroadEn_12167 SRBD1 gene, encodes complete protein.
CU689410 - Synthetic construct Homo sapiens gateway clone IMAGE:100019954 5' read SRBD1 mRNA.
MA446524 - JP 2018138019-A/18450: Polycomb-Associated Non-Coding RNAs.
AK055896 - Homo sapiens cDNA FLJ31334 fis, clone MAMGL1000132.
JD534064 - Sequence 515088 from Patent EP1572962.
JD318686 - Sequence 299710 from Patent EP1572962.
JD145362 - Sequence 126386 from Patent EP1572962.
JD433169 - Sequence 414193 from Patent EP1572962.
JD075393 - Sequence 56417 from Patent EP1572962.
LF342356 - JP 2014500723-A/149859: Polycomb-Associated Non-Coding RNAs.
MA577933 - JP 2018138019-A/149859: Polycomb-Associated Non-Coding RNAs.
JD203717 - Sequence 184741 from Patent EP1572962.
LF342406 - JP 2014500723-A/149909: Polycomb-Associated Non-Coding RNAs.
LF342411 - JP 2014500723-A/149914: Polycomb-Associated Non-Coding RNAs.
LF342412 - JP 2014500723-A/149915: Polycomb-Associated Non-Coding RNAs.
LF342414 - JP 2014500723-A/149917: Polycomb-Associated Non-Coding RNAs.
MA577983 - JP 2018138019-A/149909: Polycomb-Associated Non-Coding RNAs.
MA577988 - JP 2018138019-A/149914: Polycomb-Associated Non-Coding RNAs.
MA577989 - JP 2018138019-A/149915: Polycomb-Associated Non-Coding RNAs.
MA577991 - JP 2018138019-A/149917: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_018079, NP_060549, Q53T56, Q8N5C6, Q96TA4, Q9NW11, SRBD1_HUMAN
UCSC ID: uc002rus.3
RefSeq Accession: NM_018079
Protein: Q8N5C6 (aka SRBD1_HUMAN)
CCDS: CCDS1823.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018079.4
exon count: 21CDS single in 3' UTR: no RNA size: 3717
ORF size: 2988CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6069.00frame shift in genome: no % Coverage: 99.38
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.