Human Gene SSR1 (ENST00000244763.9_12) from GENCODE V47lift37
  Description: signal sequence receptor subunit 1, transcript variant 3 (from RefSeq NR_120448.2)
Gencode Transcript: ENST00000244763.9_12
Gencode Gene: ENSG00000124783.14_17
Transcript (Including UTRs)
   Position: hg19 chr6:7,281,376-7,313,432 Size: 32,057 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr6:7,290,097-7,313,353 Size: 23,257 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:7,281,376-7,313,432)mRNA (may differ from genome)Protein (286 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SSRA_HUMAN
DESCRIPTION: RecName: Full=Translocon-associated protein subunit alpha; Short=TRAP-alpha; AltName: Full=Signal sequence receptor subunit alpha; Short=SSR-alpha; Flags: Precursor;
FUNCTION: TRAP proteins are part of a complex whose function is to bind calcium to the ER membrane and thereby regulate the retention of ER resident proteins. May be involved in the recycling of the translocation apparatus after completion of the translocation process or may function as a membrane-bound chaperone facilitating folding of translocated proteins.
SUBUNIT: Heterotetramer of TRAP-alpha, TRAP-beta, TRAP-delta and TRAP-gamma. Interacts with palmitoylated calnexin (CALX), the interaction is required for efficient folding of glycosylated proteins.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type I membrane protein.
DOMAIN: Shows a remarkable charge distribution with the N-terminus being highly negatively charged, and the cytoplasmic C-terminus positively charged.
MISCELLANEOUS: Seems to bind calcium.
SIMILARITY: Belongs to the TRAP-alpha family.
SEQUENCE CAUTION: Sequence=CAI16444.1; 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: SSR1
Diseases sorted by gene-association score: amyotrophic lateral sclerosis 1 (1)

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

+  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: 18.01 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 439.44 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 -15.4079-0.195 Picture PostScript Text
3' UTR -2708.508721-0.311 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
IPR005595 - TRAP_alpha

Pfam Domains:
PF03896 - Translocon-associated protein (TRAP), alpha subunit

ModBase Predicted Comparative 3D Structure on P43307
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 Details 
Gene SorterGene Sorter  Gene Sorter 
 RGD  WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006613 cotranslational protein targeting to membrane
GO:0008284 positive regulation of cell proliferation
GO:0036498 IRE1-mediated unfolded protein response

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AJ420492 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1601244.
AK026687 - Homo sapiens cDNA: FLJ23034 fis, clone LNG02018.
AK024294 - Homo sapiens cDNA FLJ14232 fis, clone NT2RP4000035.
JD357931 - Sequence 338955 from Patent EP1572962.
JD244659 - Sequence 225683 from Patent EP1572962.
JD047614 - Sequence 28638 from Patent EP1572962.
JD047615 - Sequence 28639 from Patent EP1572962.
JD238370 - Sequence 219394 from Patent EP1572962.
JD238371 - Sequence 219395 from Patent EP1572962.
JD426859 - Sequence 407883 from Patent EP1572962.
JD135795 - Sequence 116819 from Patent EP1572962.
JD052727 - Sequence 33751 from Patent EP1572962.
AK025753 - Homo sapiens cDNA: FLJ22100 fis, clone HEP17127.
JD134356 - Sequence 115380 from Patent EP1572962.
JD070588 - Sequence 51612 from Patent EP1572962.
JD150902 - Sequence 131926 from Patent EP1572962.
JD376595 - Sequence 357619 from Patent EP1572962.
JD463186 - Sequence 444210 from Patent EP1572962.
JD213224 - Sequence 194248 from Patent EP1572962.
JD542965 - Sequence 523989 from Patent EP1572962.
JD560981 - Sequence 542005 from Patent EP1572962.
JD165271 - Sequence 146295 from Patent EP1572962.
JD213223 - Sequence 194247 from Patent EP1572962.
CR936719 - Homo sapiens mRNA; cDNA DKFZp781N23103 (from clone DKFZp781N23103).
AK075562 - Homo sapiens cDNA PSEC0262 fis, clone NT2RP3004505, highly similar to TRANSLOCON-ASSOCIATED PROTEIN, ALPHA SUBUNIT PRECURSOR.
AF156965 - Homo sapiens translocon-associated protein alpha subunit mRNA, complete cds.
JD250673 - Sequence 231697 from Patent EP1572962.
JD288826 - Sequence 269850 from Patent EP1572962.
JD168854 - Sequence 149878 from Patent EP1572962.
JD492534 - Sequence 473558 from Patent EP1572962.
JD280192 - Sequence 261216 from Patent EP1572962.
JD374774 - Sequence 355798 from Patent EP1572962.
JD393905 - Sequence 374929 from Patent EP1572962.
JD299848 - Sequence 280872 from Patent EP1572962.
JD420450 - Sequence 401474 from Patent EP1572962.
JD237513 - Sequence 218537 from Patent EP1572962.
JD219882 - Sequence 200906 from Patent EP1572962.
JD237675 - Sequence 218699 from Patent EP1572962.
JD261848 - Sequence 242872 from Patent EP1572962.
JD552517 - Sequence 533541 from Patent EP1572962.
JD168539 - Sequence 149563 from Patent EP1572962.
JD044715 - Sequence 25739 from Patent EP1572962.
JD289449 - Sequence 270473 from Patent EP1572962.
AK291550 - Homo sapiens cDNA FLJ78242 complete cds, highly similar to Homo sapiens signal sequence receptor, alpha (translocon-associated protein alpha), mRNA.
JD296137 - Sequence 277161 from Patent EP1572962.
BC007710 - Homo sapiens signal sequence receptor, alpha, mRNA (cDNA clone MGC:10331 IMAGE:4054116), complete cds.
AK222762 - Homo sapiens mRNA for signal sequence receptor, alpha variant, clone: HEP00909.
AK222809 - Homo sapiens mRNA for signal sequence receptor, alpha variant, clone: HEP04334.
JD524202 - Sequence 505226 from Patent EP1572962.
JD198875 - Sequence 179899 from Patent EP1572962.
JD243543 - Sequence 224567 from Patent EP1572962.
Z12830 - H.sapiens mRNA for SSR alpha subunit.
CR456961 - Homo sapiens full open reading frame cDNA clone RZPDo834B0119D for gene SSR1, signal sequence receptor, alpha (translocon-associated protein alpha); complete cds, incl. stopcodon.
KJ892203 - Synthetic construct Homo sapiens clone ccsbBroadEn_01597 SSR1 gene, encodes complete protein.
AK312653 - Homo sapiens cDNA, FLJ93042, highly similar to Homo sapiens signal sequence receptor, alpha (translocon-associated protein alpha) (SSR1), mRNA.
BT007387 - Homo sapiens signal sequence receptor, alpha (translocon-associated protein alpha) mRNA, complete cds.
DQ892751 - Synthetic construct clone IMAGE:100005381; FLH189361.01X; RZPDo839E0474D signal sequence receptor, alpha (translocon-associated protein alpha) (SSR1) gene, encodes complete protein.
EU176743 - Synthetic construct Homo sapiens clone IMAGE:100011511; FLH189360.01L; RZPDo839H10255D signal sequence receptor, alpha (translocon-associated protein alpha) (SSR1) gene, encodes complete protein.
AB464204 - Synthetic construct DNA, clone: pF1KB6326, Homo sapiens SSR1 gene for signal sequence receptor alpha, without stop codon, in Flexi system.
JD308736 - Sequence 289760 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P43307 (Reactome details) participates in the following event(s):

R-HSA-1799326 Signal-containing nascent peptide translocates to endoplasmic reticulum
R-HSA-1799329 Signal peptidase hydrolyzes signal peptide from ribosome-associated nascent protein
R-HSA-381038 XBP1(S) activates chaperone genes
R-HSA-381070 IRE1alpha activates chaperones
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane
R-HSA-381119 Unfolded Protein Response (UPR)
R-HSA-72766 Translation
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K685, ENST00000244763.1, ENST00000244763.2, ENST00000244763.3, ENST00000244763.4, ENST00000244763.5, ENST00000244763.6, ENST00000244763.7, ENST00000244763.8, NR_120448, P43307, PSEC0262, Q53GX2, Q53H19, Q5TAM3, Q6IB43, Q8NBH9, Q96IA2, Q9TNQ8, Q9UN49, SSRA_HUMAN, TRAPA, uc317epp.1, uc317epp.2
UCSC ID: ENST00000244763.9_12
RefSeq Accession: NM_003144.5
Protein: P43307 (aka SSRA_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.