Human Gene SRP9 (uc001hpg.3) Description and Page Index
  Description: Homo sapiens signal recognition particle 9kDa (SRP9), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:225,965,515-225,978,168 Size: 12,654 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr1:225,965,643-225,977,061 Size: 11,419 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:225,965,515-225,978,168)mRNA (may differ from genome)Protein (86 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: SRP09_HUMAN
DESCRIPTION: RecName: Full=Signal recognition particle 9 kDa protein; Short=SRP9;
FUNCTION: Signal-recognition-particle assembly has a crucial role in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP9 together with SRP14 and the Alu portion of the SRP RNA, constitutes the elongation arrest domain of SRP. The complex of SRP9 and SRP14 is required for SRP RNA binding.
SUBUNIT: Signal recognition particle consists of a 7S RNA molecule of 300 nucleotides and six protein subunits: SRP72, SRP68, SRP54, SRP19, SRP14 and SRP9.
SUBCELLULAR LOCATION: Cytoplasm.
SIMILARITY: Belongs to the SRP9 family.
WEB RESOURCE: Name=Wikipedia; Note=Signal recognition particle entry; URL="http://en.wikipedia.org/wiki/Signal-recognition_particle";

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 102.91 RPKM in Brain - Hypothalamus
Total median expression: 3095.30 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 -45.30128-0.354 Picture PostScript Text
3' UTR -260.121107-0.235 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
IPR008832 - Signal_recog_particle_SRP9
IPR009018 - Signal_recog_particle_SRP9/14

Pfam Domains:
PF05486 - Signal recognition particle 9 kDa protein (SRP9)

SCOP Domains:
54762 - Signal recognition particle alu RNA binding heterodimer, SRP9/14

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1E8O
- X-ray MuPIT

1E8S
- X-ray MuPIT

1RY1
- EM MuPIT


ModBase Predicted Comparative 3D Structure on P49458
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:0003723 RNA binding
GO:0005047 signal recognition particle binding
GO:0005515 protein binding
GO:0008312 7S RNA binding

Biological Process:
GO:0006614 SRP-dependent cotranslational protein targeting to membrane
GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation
GO:0045900 negative regulation of translational elongation

Cellular Component:
GO:0005737 cytoplasm
GO:0005785 signal recognition particle receptor complex
GO:0005786 signal recognition particle, endoplasmic reticulum targeting
GO:0005829 cytosol
GO:0048500 signal recognition particle


-  Descriptions from all associated GenBank mRNAs
  KJ905928 - Synthetic construct Homo sapiens clone ccsbBroadEn_15598 SRP9 gene, encodes complete protein.
KJ897603 - Synthetic construct Homo sapiens clone ccsbBroadEn_06997 SRP9 gene, encodes complete protein.
KJ892198 - Synthetic construct Homo sapiens clone ccsbBroadEn_01592 SRP9 gene, encodes complete protein.
BC066957 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:87436 IMAGE:5263635), complete cds.
BC008443 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:14657 IMAGE:4102222), complete cds.
EF488978 - Homo sapiens signal recognition particle 9 kDa isoform mRNA, complete cds.
AF070649 - Homo sapiens clone 24452 mRNA sequence.
U20998 - Homo sapiens signal recognition particle subunit 9 (SRP9) mRNA, complete cds.
BC106005 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:110981 IMAGE:6026221), complete cds.
BC021995 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:24524 IMAGE:4101294), complete cds.
BC015094 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:22694 IMAGE:3930047), complete cds.
AK289595 - Homo sapiens cDNA FLJ76514 complete cds, highly similar to Homo sapiens signal recognition particle 9kDa (SRP9), mRNA.
BC045603 - Homo sapiens, clone IMAGE:4615687, mRNA.
BC022415 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:24591 IMAGE:4243562), complete cds.
BC064351 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:75133 IMAGE:4452218), complete cds.
AL050363 - Homo sapiens mRNA; cDNA DKFZp564M2223 (from clone DKFZp564M2223).
BC067845 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone MGC:87437 IMAGE:5287027), complete cds.
DL491687 - Novel nucleic acids.
BC070305 - Homo sapiens signal recognition particle 9kDa, mRNA (cDNA clone IMAGE:3829096), **** WARNING: chimeric clone ****.
BC024171 - Homo sapiens mRNA similar to ribosomal protein L31 (cDNA clone IMAGE:4091831).
JD506736 - Sequence 487760 from Patent EP1572962.
DL491688 - Novel nucleic acids.
DL490271 - Novel nucleic acids.
BC017414 - Homo sapiens, Similar to signal recognition particle 9kD, clone IMAGE:4655251, mRNA, partial cds.
JD314679 - Sequence 295703 from Patent EP1572962.
JD022617 - Sequence 3641 from Patent EP1572962.
JD168321 - Sequence 149345 from Patent EP1572962.
JD046468 - Sequence 27492 from Patent EP1572962.
JD184490 - Sequence 165514 from Patent EP1572962.
JD197399 - Sequence 178423 from Patent EP1572962.
JD298678 - Sequence 279702 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03060 - Protein export

Reactome (by CSHL, EBI, and GO)

Protein P49458 (Reactome details) participates in the following event(s):

R-HSA-1799332 Nascent polypeptide:mRNA:ribosome complex binds signal recognition particle (SRP)
R-HSA-1799326 Signal-containing nascent peptide translocates to endoplasmic reticulum
R-HSA-1799330 The SRP receptor binds the SRP:nascent peptide:ribosome complex
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K0N0, NM_003133, NP_003124, P49458, Q6NVX0, Q8WTW0, SRP09_HUMAN
UCSC ID: uc001hpg.3
RefSeq Accession: NM_003133
Protein: P49458 (aka SRP09_HUMAN)
CCDS: CCDS1546.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003133.5
exon count: 3CDS single in 3' UTR: no RNA size: 1524
ORF size: 261CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 656.00frame shift in genome: no % Coverage: 98.16
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.