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Aliases for SEM1 Gene

Aliases for SEM1 Gene

  • SEM1, 26S Proteasome Complex Subunit 2 3
  • Split Hand/Foot Malformation (Ectrodactyly) Type 1 2 3 5
  • SHFM1 3 4 5
  • Split Hand/Foot Malformation Type 1 Protein 3 4
  • Deleted In Split Hand/Split Foot Protein 1 3 4
  • Split Hand/Foot Deleted Protein 1 3 4
  • Shfdg1 3 4
  • DSS1 3 4
  • 26S Proteasome Complex Subunit DSS1 3
  • Deleted In Split-Hand/Split-Foot 1 3
  • Deleted In Split-Hand/Foot 1 2
  • C7orf76 4
  • SHSF1 3
  • SHFD1 3
  • ECD 3

External Ids for SEM1 Gene

Previous HGNC Symbols for SEM1 Gene

  • SHFD1
  • SHFM1

Summaries for SEM1 Gene

Entrez Gene Summary for SEM1 Gene

  • The product of this gene has been localized within the split hand/split foot malformation locus SHFM1 at chromosome 7. It has been proposed to be a candidate gene for the autosomal dominant form of the heterogeneous limb developmental disorder split hand/split foot malformation type 1. In addition, it has been shown to directly interact with BRCA2. It also may play a role in the completion of the cell cycle. [provided by RefSeq, Jul 2008]

GeneCards Summary for SEM1 Gene

SEM1 (SEM1, 26S Proteasome Complex Subunit) is a Protein Coding gene. Diseases associated with SEM1 include Split Foot and Split Hand-Split Foot Malformation. Among its related pathways are RET signaling and Regulation of activated PAK-2p34 by proteasome mediated degradation.

UniProtKB/Swiss-Prot for SEM1 Gene

  • Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis (PubMed:15117943). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, DSS1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. Binds and stabilizes BRCA2 and is thus involved in the control of R-loop-associated DNA damage and thus transcription-associated genomic instability. R-loop accumulation increases in DSS1-depleted cells.

Gene Wiki entry for SEM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEM1 Gene

Genomics for SEM1 Gene

Regulatory Elements for SEM1 Gene

Enhancers for SEM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07F097116 0.2 ENCODE 18.3 -408.1 -408116 3.6 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ENSG00000231859 SEM1 SDHAF3 HMGB3P21
GH07F096666 0.8 FANTOM5 11.3 +43.3 43321 0.2 C7orf76 SEM1 LOC100506136
GH07F096708 1 ENCODE 11 +0.4 445 2.3 HDGF CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF143 ZNF263 SEM1 C7orf76 LOC100506136
GH07F096833 0.6 ENCODE 10.7 -124.0 -124001 1.4 MLX THRB ZSCAN9 DNMT3B RARA CREM MIXL1 THAP11 HMG20B CEBPB SEM1 C7orf76 DLX6 MARK2P10 LOC105375414
GH07F096596 0.2 ENCODE 10.5 +113.2 113228 0.2 L3MBTL2 ZNF341 MYNN JUNB TCF7 PRDM10 MNT C7orf76 SEM1 GC07M096611 LOC105375412
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around SEM1 on UCSC Golden Path with GeneCards custom track

Promoters for SEM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000067904 491 2400 HDGF CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF143 ZNF263

Genomic Location for SEM1 Gene

Chromosome:
7
Start:
96,481,626 bp from pter
End:
96,709,891 bp from pter
Size:
228,266 bases
Orientation:
Minus strand

Genomic View for SEM1 Gene

Genes around SEM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEM1 Gene

Proteins for SEM1 Gene

  • Protein details for SEM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P60896-DSS1_HUMAN
    Recommended name:
    26S proteasome complex subunit DSS1
    Protein Accession:
    P60896
    Secondary Accessions:
    • Q13437
    • Q61067

    Protein attributes for SEM1 Gene

    Size:
    70 amino acids
    Molecular mass:
    8278 Da
    Quaternary structure:
    • Part of the 26S proteasome. Belongs to the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, DSS1, and either centrin CETN2 or CETN3 (PubMed:22307388). Interacts with the C-terminal of BRCA2 (PubMed:21719596).

    Three dimensional structures from OCA and Proteopedia for SEM1 Gene

  • Protein details for SEM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZVN7-CG076_HUMAN
    Recommended name:
    Putative uncharacterized protein C7orf76
    Protein Accession:
    Q6ZVN7

    Protein attributes for SEM1 Gene

    Size:
    128 amino acids
    Molecular mass:
    14085 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SEM1 Gene

Post-translational modifications for SEM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SEM1 Gene

Domains & Families for SEM1 Gene

Gene Families for SEM1 Gene

Protein Domains for SEM1 Gene

ProtoNet:
InterPro:

Graphical View of Domain Structure for InterPro Entry

P60896

UniProtKB/Swiss-Prot:

CG076_HUMAN :
  • Belongs to the DSS1/SEM1 family.
Family:
  • Belongs to the DSS1/SEM1 family.
genes like me logo Genes that share domains with SEM1: view

Function for SEM1 Gene

Molecular function for SEM1 Gene

UniProtKB/Swiss-Prot Function:
Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis (PubMed:15117943). Component of the TREX-2 complex (transcription and export complex 2), composed of at least ENY2, GANP, PCID2, DSS1, and either centrin CETN2 or CETN3 (PubMed:22307388). The TREX-2 complex functions in docking export-competent ribonucleoprotein particles (mRNPs) to the nuclear entrance of the nuclear pore complex (nuclear basket). TREX-2 participates in mRNA export and accurate chromatin positioning in the nucleus by tethering genes to the nuclear periphery. Binds and stabilizes BRCA2 and is thus involved in the control of R-loop-associated DNA damage and thus transcription-associated genomic instability. R-loop accumulation increases in DSS1-depleted cells.

Gene Ontology (GO) - Molecular Function for SEM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 10373512
genes like me logo Genes that share ontologies with SEM1: view
genes like me logo Genes that share phenotypes with SEM1: view

Human Phenotype Ontology for SEM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for SEM1 Gene

miRTarBase miRNAs that target SEM1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SEM1 Gene

Localization for SEM1 Gene

Gene Ontology (GO) - Cellular Components for SEM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000502 proteasome complex IDA 15117943
GO:0008541 proteasome regulatory particle, lid subcomplex IEA --
GO:0032039 colocalizes_with integrator complex IDA 16239144
genes like me logo Genes that share ontologies with SEM1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from COMPARTMENTS for SEM1 Gene

Pathways & Interactions for SEM1 Gene

SuperPathways for SEM1 Gene

SuperPathway Contained pathways
1 Regulation of activated PAK-2p34 by proteasome mediated degradation
.78
.32
2 RET signaling
3 HIV Life Cycle
.45
4 Class I MHC mediated antigen processing and presentation
5 Cell Cycle, Mitotic
.60
genes like me logo Genes that share pathways with SEM1: view

Gene Ontology (GO) - Biological Process for SEM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IBA --
GO:0006406 mRNA export from nucleus IEA --
GO:0006508 proteolysis IBA --
GO:0043248 proteasome assembly IEA --
genes like me logo Genes that share ontologies with SEM1: view

No data available for SIGNOR curated interactions for SEM1 Gene

Transcripts for SEM1 Gene

Unigene Clusters for SEM1 Gene

Split hand/foot malformation (ectrodactyly) type 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEM1 Gene

No ASD Table

Relevant External Links for SEM1 Gene

GeneLoc Exon Structure for
SEM1
ECgene alternative splicing isoforms for
SEM1

Expression for SEM1 Gene

NURSA nuclear receptor signaling pathways regulating expression of SEM1 Gene:

SEM1

SOURCE GeneReport for Unigene cluster for SEM1 Gene:

Hs.489201

mRNA Expression by UniProt/SwissProt for SEM1 Gene:

P60896-DSS1_HUMAN
Tissue specificity: Expressed in limb bud, craniofacial primordia and skin.

Primer Products

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression and Protein tissue co-expression partners for SEM1 Gene

Orthologs for SEM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SEM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SHFM1 34 35
  • 100 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SHFM1 35
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SHFM1 34 35
  • 93.33 (n)
mouse
(Mus musculus)
Mammalia Shfm1 34 16 35
  • 88.57 (n)
rat
(Rattus norvegicus)
Mammalia Shfm1 34
  • 88.57 (n)
dog
(Canis familiaris)
Mammalia SHFM1 35
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves SHFM1 34 35
  • 85.71 (n)
lizard
(Anolis carolinensis)
Reptilia SHFM1 35
  • 100 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii shfm1 34 35
  • 79.05 (n)
wufb55c02 34
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1217 34
Species where no ortholog for SEM1 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SEM1 Gene

ENSEMBL:
Gene Tree for SEM1 (if available)
TreeFam:
Gene Tree for SEM1 (if available)

Paralogs for SEM1 Gene

Pseudogenes.org Pseudogenes for SEM1 Gene

genes like me logo Genes that share paralogs with SEM1: view

No data available for Paralogs for SEM1 Gene

Variants for SEM1 Gene

Sequence variations from dbSNP and Humsavar for SEM1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
rs10228128 -- 96,707,362(+) AATAT(C/T)GAGTG intron-variant
rs10233126 -- 96,703,080(+) gatca(C/T)acagg intron-variant
rs10233528 -- 96,703,466(+) aaaaa(C/T)tatat intron-variant
rs10242202 -- 96,707,590(+) AATAA(A/G)CAAGT intron-variant
rs10249092 -- 96,691,292(+) CCTGC(G/T)ACATG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SEM1 Gene

Variant ID Type Subtype PubMed ID
nsv831065 CNV gain 17160897

Variation tolerance for SEM1 Gene

Residual Variation Intolerance Score: 59.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.01; 0.34% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SEM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEM1 Gene

Disorders for SEM1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SEM1 Gene - From: Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SEM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SEM1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SEM1
genes like me logo Genes that share disorders with SEM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SEM1 Gene

Publications for SEM1 Gene

  1. Characterization of the split hand/split foot malformation locus SHFM1 at 7q21.3-q22.1 and analysis of a candidate gene for its expression during limb development. (PMID: 8733122) Crackower M.A. … Tsui L.-C. (Hum. Mol. Genet. 1996) 2 3 4 64
  2. A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell-based assay. (PMID: 21719596) Biswas K. … Sharan S.K. (Blood 2011) 3 4 64
  3. Mass spectrometric characterization of the affinity-purified human 26S proteasome complex. (PMID: 17323924) Wang X. … Huang L. (Biochemistry 2007) 3 4 64
  4. The proteasome is involved in determining differential utilization of double-strand break repair pathways. (PMID: 17563742) Gudmundsdottir K. … Ashworth A. (Oncogene 2007) 3 22 64
  5. Sem1p is a novel subunit of the 26S proteasome from Saccharomyces cerevisiae. (PMID: 15117943) Sone T. … Yokosawa H. (J. Biol. Chem. 2004) 3 4 64

Products for SEM1 Gene

Sources for SEM1 Gene

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