Human Gene SRBD1 (ENST00000263736.5_7) from GENCODE V47lift37
  Description: S1 RNA binding domain 1 (from RefSeq NM_018079.5)
Gencode Transcript: ENST00000263736.5_7
Gencode Gene: ENSG00000068784.13_9
Transcript (Including UTRs)
   Position: hg19 chr2:45,615,819-45,838,406 Size: 222,588 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 CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:45,615,819-45,838,406)mRNA (may differ from genome)Protein (995 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIPubMedUniProtKBBioGrid CRISPR DB

-  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;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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
  Press "+" in the title bar above to open this section.

-  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
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -14.1049-0.288 Picture PostScript Text
3' UTR -118.00630-0.187 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
PF17674 - HHH domain

SCOP Domains:
158832 - Tex N-terminal region-like
81585 - PsbU/PolX domain-like
47781 - RuvA domain 2-like
50249 - Nucleic acid-binding proteins
53098 - Ribonuclease H-like

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 orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  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: ENST00000263736.1, ENST00000263736.2, ENST00000263736.3, ENST00000263736.4, NM_018079, Q53T56, Q8N5C6, Q96TA4, Q9NW11, SRBD1_HUMAN, uc317hmc.1, uc317hmc.2
UCSC ID: ENST00000263736.5_7
RefSeq Accession: NM_018079.5
Protein: Q8N5C6 (aka SRBD1_HUMAN)

-  Gene Model Information
  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.