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Aliases for SHFM1 Gene

Aliases for SHFM1 Gene

  • Split Hand/Foot Malformation (Ectrodactyly) Type 1 5 2 3
  • 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
  • Deleted In Split-Hand/Split-Foot 1 3
  • Deleted In Split-Hand/Foot 1 2
  • SHSF1 3
  • SHFD1 3
  • SEM1 3
  • ECD 3

External Ids for SHFM1 Gene

Previous HGNC Symbols for SHFM1 Gene

  • SHFD1

Previous GeneCards Identifiers for SHFM1 Gene

  • GC07U990090
  • GC07M095713
  • GC07M095929
  • GC07M095962
  • GC07M096156
  • GC07M090925

Summaries for SHFM1 Gene

Entrez Gene Summary for SHFM1 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 SHFM1 Gene

SHFM1 (Split Hand/Foot Malformation (Ectrodactyly) Type 1) is a Protein Coding gene. Diseases associated with SHFM1 include split foot and split hand. Among its related pathways are Epstein-Barr virus infection and Homologous recombination.

UniProtKB/Swiss-Prot for SHFM1 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 SHFM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SHFM1 Gene

Genomics for SHFM1 Gene

Regulatory Elements for SHFM1 Gene

Enhancers for SHFM1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SHFM1 on UCSC Golden Path with GeneCards custom track

Promoters for SHFM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SHFM1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SHFM1 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 SHFM1 Gene

Genes around SHFM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHFM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHFM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SHFM1 Gene

Proteins for SHFM1 Gene

  • Protein details for SHFM1 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 SHFM1 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 SHFM1 Gene

neXtProt entry for SHFM1 Gene

Proteomics data for SHFM1 Gene at MOPED

Post-translational modifications for SHFM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for SHFM1 Gene

Domains & Families for SHFM1 Gene

Protein Domains for SHFM1 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

P60896

UniProtKB/Swiss-Prot:

DSS1_HUMAN :
  • Belongs to the DSS1/SEM1 family.
Family:
  • Belongs to the DSS1/SEM1 family.
genes like me logo Genes that share domains with SHFM1: view

No data available for Gene Families for SHFM1 Gene

Function for SHFM1 Gene

Molecular function for SHFM1 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.
genes like me logo Genes that share phenotypes with SHFM1: view

Human Phenotype Ontology for SHFM1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for SHFM1 Gene

Localization for SHFM1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SHFM1 Gene COMPARTMENTS Subcellular localization image for SHFM1 gene
Compartment Confidence
extracellular 3
nucleus 3
cytosol 2

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for SHFM1 Gene

Pathways & Interactions for SHFM1 Gene

genes like me logo Genes that share pathways with SHFM1: view

Pathways by source for SHFM1 Gene

Gene Ontology (GO) - Biological Process for SHFM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000724 double-strand break repair via homologous recombination IBA --
GO:0006508 proteolysis IBA --
genes like me logo Genes that share ontologies with SHFM1: view

No data available for SIGNOR curated interactions for SHFM1 Gene

Drugs & Compounds for SHFM1 Gene

No Compound Related Data Available

Transcripts for SHFM1 Gene

Unigene Clusters for SHFM1 Gene

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

Alternative Splicing Database (ASD) splice patterns (SP) for SHFM1 Gene

No ASD Table

Relevant External Links for SHFM1 Gene

GeneLoc Exon Structure for
SHFM1
ECgene alternative splicing isoforms for
SHFM1

Expression for SHFM1 Gene

mRNA expression in normal human tissues for SHFM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SHFM1 Gene

This gene is overexpressed in Spleen (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SHFM1 Gene



SOURCE GeneReport for Unigene cluster for SHFM1 Gene Hs.489201

mRNA Expression by UniProt/SwissProt for SHFM1 Gene

P60896-DSS1_HUMAN
Tissue specificity: Expressed in limb bud, craniofacial primordia and skin.
genes like me logo Genes that share expression patterns with SHFM1: view

Protein tissue co-expression partners for SHFM1 Gene

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for SHFM1 Gene

Orthologs for SHFM1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SHFM1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SHFM1 35
  • 93.33 (n)
  • 100 (a)
SHFM1 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Shfm1 35
  • 88.57 (n)
  • 100 (a)
Shfm1 16
Shfm1 36
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SHFM1 35
  • 100 (n)
  • 100 (a)
SHFM1 36
  • 65 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Shfm1 35
  • 88.57 (n)
  • 100 (a)
dog
(Canis familiaris)
Mammalia SHFM1 36
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SHFM1 36
  • 97 (a)
OneToOne
chicken
(Gallus gallus)
Aves SHFM1 35
  • 85.71 (n)
  • 98.57 (a)
SHFM1 36
  • 99 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SHFM1 36
  • 100 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii shfm1 35
  • 79.05 (n)
  • 97.14 (a)
wufb55c02 35
shfm1 36
  • 97 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1217 35
Species with no ortholog for SHFM1:
  • 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 SHFM1 Gene

ENSEMBL:
Gene Tree for SHFM1 (if available)
TreeFam:
Gene Tree for SHFM1 (if available)

Paralogs for SHFM1 Gene

No data available for Paralogs for SHFM1 Gene

Variants for SHFM1 Gene

Sequence variations from dbSNP and Humsavar for SHFM1 Gene

SNP ID Clin Chr 07 pos Sequence Context AA Info Type
VAR_012003 -
rs1404505 -- 96,691,610(+) TGATA(C/T)TATGT intron-variant
rs12669989 -- 96,697,008(+) GATAT(C/T)TGATA intron-variant
rs1534078 -- 96,701,255(-) TTTTT(G/T)GGGGG intron-variant
rs12690924 -- 96,699,531(+) AGGCC(A/G)CAAAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SHFM1 Gene

Variant ID Type Subtype PubMed ID
nsv888756 CNV Gain 21882294
nsv831065 CNV Gain 17160897

Variation tolerance for SHFM1 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 SHFM1 Gene

HapMap Linkage Disequilibrium report
SHFM1
Human Gene Mutation Database (HGMD)
SHFM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHFM1 Gene

Disorders for SHFM1 Gene

MalaCards: The human disease database

(11) MalaCards diseases for SHFM1 Gene - From: Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SHFM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SHFM1

Genetic Association Database (GAD)
SHFM1
Human Genome Epidemiology (HuGE) Navigator
SHFM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SHFM1
genes like me logo Genes that share disorders with SHFM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SHFM1 Gene

Publications for SHFM1 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 67
  2. The proteasome is involved in determining differential utilization of double-strand break repair pathways. (PMID: 17563742) Gudmundsdottir K. … Ashworth A. (Oncogene 2007) 3 23
  3. SEM1, a homologue of the split hand/split foot malformation candidate gene Dss1, regulates exocytosis and pseudohyphal differentiation in yeast. (PMID: 9927667) JAontti J. … KerAonen S. (Proc. Natl. Acad. Sci. U.S.A. 1999) 3 23
  4. Bilateral split hand and split foot malformation in a boy with a de novo interstitial deletion of 7q21.3. (PMID: 1895319) Roberts S.H. … Meredith A.L. (J. Med. Genet. 1991) 2 3
  5. The contribution of common genetic variation to nicotine and cotinine glucuronidation in multiple ethnic/racial populations. (PMID: 25293881) Patel Y.M. … Murphy S.E. (Cancer Epidemiol. Biomarkers Prev. 2015) 3

Products for SHFM1 Gene

Sources for SHFM1 Gene

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