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Aliases for SSR4 Gene

Aliases for SSR4 Gene

  • Signal Sequence Receptor Subunit 4 2 3 5
  • Signal Sequence Receptor, Delta 2 3
  • TRAP-Delta 3 4
  • SSR-Delta 3 4
  • TRAPD 3 4
  • Translocon-Associated Protein Subunit Delta 3
  • Signal Sequence Receptor Subunit Delta 4
  • Translocon-Associated Protein Delta 2
  • CDG1Y 3

External Ids for SSR4 Gene

Previous GeneCards Identifiers for SSR4 Gene

  • GC0XP147197
  • GC0XP149515
  • GC0XP150644
  • GC0XP151526
  • GC0XP151527
  • GC0XP152579
  • GC0XP152712
  • GC0XP153058
  • GC0XP141717

Summaries for SSR4 Gene

Entrez Gene Summary for SSR4 Gene

  • This gene encodes the delta subunit of the translocon-associated protein complex which is involved in translocating proteins across the endoplasmic reticulum membrane. The encoded protein is located in the Xq28 region and is arranged in a compact head-to-head manner with the isocitrate dehydrogenase 3 (NAD+) gamma gene and both genes are driven by a CpG-embedded bidirectional promoter. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2011]

GeneCards Summary for SSR4 Gene

SSR4 (Signal Sequence Receptor Subunit 4) is a Protein Coding gene. Diseases associated with SSR4 include Congenital Disorder Of Glycosylation, Type Iy and Ssr4-Cdg. Among its related pathways are Gene Expression and Viral mRNA Translation.

UniProtKB/Swiss-Prot for SSR4 Gene

  • 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.

Gene Wiki entry for SSR4 Gene

Additional gene information for SSR4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SSR4 Gene

Genomics for SSR4 Gene

GeneHancer (GH) Regulatory Elements for SSR4 Gene

Promoters and enhancers for SSR4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XI153792 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 +0.9 863 3.3 PKNOX1 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF143 FOS SP3 IDH3G SSR4 PLXNB3 SRPK3
GH0XI153884 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE 13.3 +92.6 92589 3 CTCF KLF1 MAX KLF17 ZIC2 RAD21 HIC1 ZFHX2 GATA3 GLIS2 L1CAM RENBP TMEM187 PDZD4 IDH3G SSR4 SRPK3 PLXNB3 ARHGAP4 NAA10
GH0XI153844 Enhancer 0.6 ENCODE 13.7 +52.2 52163 1.8 MEIS2 BACH1 MAFG SP1 ZNF316 ZNF143 EMSY MAFK SSR4 IDH3G SRPK3 PLXNB3 L1CAM ABCD1 BCAP31 FAM3A CYCSP45 GC0XM153869
GH0XI153854 Enhancer 0.4 ENCODE 13.5 +61.3 61345 0.2 CTCF HLF L1CAM PDZD4 AVPR2 IDH3G SSR4 SRPK3 PLXNB3 ABCD1 BCAP31 CYCSP45
GH0XI153780 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 0.4 -11.9 -11925 2.5 HDGF CTCF KLF1 ZNF449 ZIC2 RAD21 BCL11B ZFHX2 GLIS2 PATZ1 SRPK3 PLXNB3 SSR4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SSR4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SSR4 gene promoter:

Genomic Locations for SSR4 Gene

Genomic Locations for SSR4 Gene
chrX:153,793,516-153,798,512
(GRCh38/hg38)
Size:
4,997 bases
Orientation:
Plus strand
chrX:153,058,971-153,063,967
(GRCh37/hg19)

Genomic View for SSR4 Gene

Genes around SSR4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SSR4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SSR4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SSR4 Gene

Proteins for SSR4 Gene

  • Protein details for SSR4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51571-SSRD_HUMAN
    Recommended name:
    Translocon-associated protein subunit delta
    Protein Accession:
    P51571
    Secondary Accessions:
    • A8K378
    • Q53XY1

    Protein attributes for SSR4 Gene

    Size:
    173 amino acids
    Molecular mass:
    18999 Da
    Quaternary structure:
    • Heterotetramer of TRAP-alpha, TRAP-beta, TRAP-delta and TRAP-gamma.

neXtProt entry for SSR4 Gene

Post-translational modifications for SSR4 Gene

  • Ubiquitination at isoforms=73 and isoforms=95

No data available for DME Specific Peptides for SSR4 Gene

Domains & Families for SSR4 Gene

Gene Families for SSR4 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted membrane proteins

Protein Domains for SSR4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SSR4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P51571

UniProtKB/Swiss-Prot:

SSRD_HUMAN :
  • Belongs to the TRAP-delta family.
Family:
  • Belongs to the TRAP-delta family.
genes like me logo Genes that share domains with SSR4: view

Function for SSR4 Gene

Molecular function for SSR4 Gene

GENATLAS Biochemistry:
signal sequence receptor delta,with an alternative polyadenylation site,expressed in many tissues
UniProtKB/Swiss-Prot 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.
genes like me logo Genes that share phenotypes with SSR4: view

Human Phenotype Ontology for SSR4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for SSR4 Gene

miRTarBase miRNAs that target SSR4

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for SSR4 Gene

Localization for SSR4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SSR4 Gene

Endoplasmic reticulum membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SSR4 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 5
plasma membrane 2

Gene Ontology (GO) - Cellular Components for SSR4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005784 Sec61 translocon complex NAS 7492314
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome IDA,HDA 20458337
genes like me logo Genes that share ontologies with SSR4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SSR4 Gene

Pathways & Interactions for SSR4 Gene

genes like me logo Genes that share pathways with SSR4: view

Pathways by source for SSR4 Gene

Gene Ontology (GO) - Biological Process for SSR4 Gene

None

No data available for SIGNOR curated interactions for SSR4 Gene

Drugs & Compounds for SSR4 Gene

(1) Drugs for SSR4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with SSR4: view

Transcripts for SSR4 Gene

Unigene Clusters for SSR4 Gene

Signal sequence receptor, delta:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SSR4 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c · 5d · 5e ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10a · 10b
SP1: - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - - - - -
SP4: -
SP5: - - - - - - - -
SP6: - - - - - - - - - - -
SP7:
SP8: - - - - - - -
SP9: - - - -
SP10: - - - - - - - - - - - -
SP11: - - - -
SP12: -

Relevant External Links for SSR4 Gene

GeneLoc Exon Structure for
SSR4
ECgene alternative splicing isoforms for
SSR4

Expression for SSR4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SSR4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SSR4 Gene

This gene is overexpressed in Pancreas (x4.1).

Protein differential expression in normal tissues from HIPED for SSR4 Gene

This gene is overexpressed in Nasal epithelium (9.8) and Bone (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SSR4 Gene



Protein tissue co-expression partners for SSR4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SSR4 Gene:

SSR4

SOURCE GeneReport for Unigene cluster for SSR4 Gene:

Hs.409223

Evidence on tissue expression from TISSUES for SSR4 Gene

  • Nervous system(4.7)
  • Liver(4.4)
  • Spleen(4.4)
  • Blood(4.3)
  • Lung(3.1)
  • Pancreas(3.1)
  • Stomach(2.5)
  • Intestine(2.4)
  • Bone marrow(2.2)
  • Lymph node(2.2)
  • Skin(2.2)
  • Adrenal gland(2.1)
  • Thyroid gland(2.1)
  • Gall bladder(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SSR4 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • chin
  • ear
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • skull
Thorax:
  • heart
Pelvis:
  • penis
  • urethra
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • blood vessel
  • skin
genes like me logo Genes that share expression patterns with SSR4: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for SSR4 Gene

Orthologs for SSR4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SSR4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SSR4 33 34
  • 99.09 (n)
dog
(Canis familiaris)
Mammalia SSR4 33 34
  • 90.67 (n)
cow
(Bos Taurus)
Mammalia SSR4 33 34
  • 88 (n)
rat
(Rattus norvegicus)
Mammalia Ssr4 33
  • 87.56 (n)
mouse
(Mus musculus)
Mammalia Ssr4 33 16 34
  • 86.44 (n)
oppossum
(Monodelphis domestica)
Mammalia SSR4 34
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 70 (a)
OneToMany
-- 34
  • 65 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia SSR4 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ssr4 33
  • 72 (n)
zebrafish
(Danio rerio)
Actinopterygii ssr4 33 34
  • 67.33 (n)
wufe06a08 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9584 33
fruit fly
(Drosophila melanogaster)
Insecta Tapdelta 34 33
  • 49.3 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea trap-4 33 34
  • 49.64 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7940 34
  • 40 (a)
OneToOne
Species where no ortholog for SSR4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SSR4 Gene

ENSEMBL:
Gene Tree for SSR4 (if available)
TreeFam:
Gene Tree for SSR4 (if available)

Paralogs for SSR4 Gene

Pseudogenes.org Pseudogenes for SSR4 Gene

genes like me logo Genes that share paralogs with SSR4: view

No data available for Paralogs for SSR4 Gene

Variants for SSR4 Gene

Sequence variations from dbSNP and Humsavar for SSR4 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1057518735 pathogenic, Congenital disorder of glycosylation type 1y 153,798,137(+) G/A splice_donor_variant
rs1057518736 pathogenic, Congenital disorder of glycosylation type 1y 153,798,328(+) G/A splice_acceptor_variant
rs606231298 pathogenic, Congenital disorder of glycosylation type 1y 153,797,779(+) TT/T coding_sequence_variant, frameshift, non_coding_transcript_variant
rs794729223 conflicting-interpretations-of-pathogenicity, Congenital disorder of glycosylation type 1y 153,798,075(+) AGAG/AG coding_sequence_variant, frameshift, non_coding_transcript_variant
rs139415367 likely-benign, not specified 153,796,486(+) C/T 5_prime_UTR_variant, coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SSR4 Gene

Variant ID Type Subtype PubMed ID
esv33199 CNV gain+loss 17666407

Variation tolerance for SSR4 Gene

Residual Variation Intolerance Score: 25.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.25; 5.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SSR4 Gene

Human Gene Mutation Database (HGMD)
SSR4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SSR4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SSR4 Gene

Disorders for SSR4 Gene

MalaCards: The human disease database

(6) MalaCards diseases for SSR4 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SSR4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SSRD_HUMAN
  • Congenital disorder of glycosylation 1Y (CDG1Y) [MIM:300934]: A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. {ECO:0000269 PubMed:24218363}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SSR4

genes like me logo Genes that share disorders with SSR4: view

No data available for Genatlas for SSR4 Gene

Publications for SSR4 Gene

  1. Genomic organization of two novel genes on human Xq28: compact head to head arrangement of IDH gamma and TRAP delta is conserved in rat and mouse. (PMID: 9286695) Brenner V … Platzer M (Genomics 1997) 2 3 4 22 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. NEDL1, a novel ubiquitin-protein isopeptide ligase for dishevelled-1, targets mutant superoxide dismutase-1. (PMID: 14684739) Miyazaki K … Nakagawara A (The Journal of biological chemistry 2004) 3 22 58
  5. Cloning and molecular characterization of a human ortholog of Monodelphis TRAPD in ultraviolet B-induced melanoma. (PMID: 15057039) Wang Z … VandeBerg JL (Melanoma research 2004) 3 22 58

Products for SSR4 Gene

Sources for SSR4 Gene

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