Human Gene SHFM1 (uc003uoi.3) Description and Page Index
  Description: Homo sapiens split hand/foot malformation (ectrodactyly) type 1 (SHFM1), mRNA.
RefSeq Summary (NM_006304): 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].
Transcript (Including UTRs)
   Position: hg19 chr7:96,318,079-96,339,203 Size: 21,125 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr7:96,318,236-96,339,075 Size: 20,840 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:96,318,079-96,339,203)mRNA (may differ from genome)Protein (70 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DSS1_HUMAN
DESCRIPTION: RecName: Full=26S proteasome complex subunit DSS1; AltName: Full=Deleted in split hand/split foot protein 1; AltName: Full=Split hand/foot deleted protein 1; AltName: Full=Split hand/foot malformation type 1 protein;
FUNCTION: Subunit of the 26S proteasome which plays a role in ubiquitin-dependent proteolysis.
SUBUNIT: Part of the 26S proteasome. Interacts with the C-terminal of BRCA2.
INTERACTION: P51587:BRCA2; NbExp=4; IntAct=EBI-79819, EBI-79792;
TISSUE SPECIFICITY: Expressed in limb bud, craniofacial primordia and skin.
SIMILARITY: Belongs to the DSS1/SEM1 family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SHFM1";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SHFM1
CDC HuGE Published Literature: SHFM1
Positive Disease Associations: Immunoglobulin A , Response to radiation
Related Studies:
  1. Immunoglobulin A
    Ricardo C Ferreira et al. Nature genetics 2010, Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency., Nature genetics. [PubMed 20694011]
  2. Response to radiation
    Nifang Niu et al. Genome research 2010, Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines., Genome research. [PubMed 20923822]

-  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: 38.09 RPKM in Testis
Total median expression: 989.54 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 -38.10128-0.298 Picture PostScript Text
3' UTR -32.24157-0.205 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
IPR007834 - DSS1_SEM1

Pfam Domains:
PF05160 - DSS1/SEM1 family

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

1IYJ
- X-ray MuPIT

1MIU
- X-ray MuPIT

1MJE
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3T5X - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P60896
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 BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

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

Biological Process:
GO:0006406 mRNA export from nucleus
GO:0016579 protein deubiquitination
GO:0043248 proteasome assembly
GO:0043687 post-translational protein modification

Cellular Component:
GO:0000502 proteasome complex
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0008541 proteasome regulatory particle, lid subcomplex
GO:0032039 integrator complex


-  Descriptions from all associated GenBank mRNAs
  AK309241 - Homo sapiens cDNA, FLJ99282.
AK291070 - Homo sapiens cDNA FLJ76393 complete cds, highly similar to Homo sapiens split hand/foot malformation (ectrodactyly) type 1 (SHFM1), mRNA.
U41515 - Human deleted in split hand/split foot 1 (DSS1) mRNA, complete cds.
BC032782 - Homo sapiens split hand/foot malformation (ectrodactyly) type 1, mRNA (cDNA clone MGC:45216 IMAGE:5166837), complete cds.
KJ892456 - Synthetic construct Homo sapiens clone ccsbBroadEn_01850 SHFM1 gene, encodes complete protein.
CR456887 - Homo sapiens full open reading frame cDNA clone RZPDo834B0916D for gene SHFM1, split hand/foot malformation (ectrodactyly) type 1; complete cds, incl. stopcodon.
AK094899 - Homo sapiens cDNA FLJ37580 fis, clone BRCOC2004036.
JD273395 - Sequence 254419 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03050 - Proteasome
hsa03440 - Homologous recombination

BioCyc Knowledge Library
PWY3DJ-213 - Targeted protein degradation

Reactome (by CSHL, EBI, and GO)

Protein P60896 (Reactome details) participates in the following event(s):

R-HSA-5665871 ADRM1 binds 26S proteasome
R-HSA-8956140 NEDD8 and UBD bind NUB1 and the 26S proteasome
R-HSA-5665854 ADRM1:26S proteaseome binds UCHL5
R-HSA-5689539 ADRM1:26S proteaseome binds USP14
R-HSA-5689603 UCH proteinases
R-HSA-8951664 Neddylation
R-HSA-174084 Autodegradation of Cdh1 by Cdh1:APC/C
R-HSA-187577 SCF(Skp2)-mediated degradation of p27/p21
R-HSA-5632684 Hedgehog 'on' state
R-HSA-8939902 Regulation of RUNX2 expression and activity
R-HSA-8941858 Regulation of RUNX3 expression and activity
R-HSA-5689880 Ub-specific processing proteases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-68827 CDT1 association with the CDC6:ORC:origin complex
R-HSA-68949 Orc1 removal from chromatin
R-HSA-69017 CDK-mediated phosphorylation and removal of Cdc6
R-HSA-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-HSA-69229 Ubiquitin-dependent degradation of Cyclin D1
R-HSA-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
R-HSA-174154 APC/C:Cdc20 mediated degradation of Securin
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1
R-HSA-174184 Cdc20:Phospho-APC/C mediated degradation of Cyclin A
R-HSA-180534 Vpu mediated degradation of CD4
R-HSA-180585 Vif-mediated degradation of APOBEC3G
R-HSA-9020702 Interleukin-1 signaling
R-HSA-211733 Regulation of activated PAK-2p34 by proteasome mediated degradation
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-HSA-350562 Regulation of ornithine decarboxylase (ODC)
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1169091 Activation of NF-kappaB in B cells
R-HSA-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-HSA-1236974 ER-Phagosome pathway
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes)
R-HSA-4641258 Degradation of DVL
R-HSA-195253 Degradation of beta-catenin by the destruction complex
R-HSA-4641257 Degradation of AXIN
R-HSA-4608870 Asymmetric localization of PCP proteins
R-HSA-5358346 Hedgehog ligand biogenesis
R-HSA-5362768 Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
R-HSA-202424 Downstream TCR signaling
R-HSA-2871837 FCERI mediated NF-kB activation
R-HSA-5607764 CLEC7A (Dectin-1) signaling
R-HSA-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-HSA-5676590 NIK-->noncanonical NF-kB signaling
R-HSA-5610785 GLI3 is processed to GLI3R by the proteasome
R-HSA-5610783 Degradation of GLI2 by the proteasome
R-HSA-5610780 Degradation of GLI1 by the proteasome
R-HSA-5658442 Regulation of RAS by GAPs
R-HSA-5668541 TNFR2 non-canonical NF-kB pathway
R-HSA-5687128 MAPK6/MAPK4 signaling
R-HSA-8948751 Regulation of PTEN stability and activity
R-HSA-69481 G2/M Checkpoints
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-HSA-382556 ABC-family proteins mediated transport
R-HSA-5678895 Defective CFTR causes cystic fibrosis
R-HSA-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-HSA-9010553 Regulation of expression of SLITs and ROBOs
R-HSA-174143 APC/C-mediated degradation of cell cycle proteins
R-HSA-69202 Cyclin E associated events during G1/S transition
R-HSA-69656 Cyclin A:Cdk2-associated events at S phase entry
R-HSA-5358351 Signaling by Hedgehog
R-HSA-8878166 Transcriptional regulation by RUNX2
R-HSA-8878159 Transcriptional regulation by RUNX3
R-HSA-392499 Metabolism of proteins
R-HSA-68867 Assembly of the pre-replicative complex
R-HSA-69052 Switching of origins to a post-replicative state
R-HSA-69610 p53-Independent DNA Damage Response
R-HSA-75815 Ubiquitin-dependent degradation of Cyclin D
R-HSA-176409 APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-68882 Mitotic Anaphase
R-HSA-176408 Regulation of APC/C activators between G1/S and early anaphase
R-HSA-179419 APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint
R-HSA-162909 Host Interactions of HIV factors
R-HSA-446652 Interleukin-1 family signaling
R-HSA-169911 Regulation of Apoptosis
R-HSA-69541 Stabilization of p53
R-HSA-351202 Metabolism of polyamines
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR)
R-HSA-1234174 Regulation of Hypoxia-inducible Factor (HIF) by oxygen
R-HSA-1236975 Antigen processing-Cross presentation
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-4086400 PCP/CE pathway
R-HSA-5387390 Hh mutants abrogate ligand secretion
R-HSA-202403 TCR signaling
R-HSA-2454202 Fc epsilon receptor (FCERI) signaling
R-HSA-5621481 C-type lectin receptors (CLRs)
R-HSA-5610787 Hedgehog 'off' state
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-5683057 MAPK family signaling cascades
R-HSA-6807070 PTEN Regulation
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-69275 G2/M Transition
R-HSA-382551 Transport of small molecules
R-HSA-5619084 ABC transporter disorders
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-376176 Signaling by ROBO receptors
R-HSA-453276 Regulation of mitotic cell cycle
R-HSA-69206 G1/S Transition
R-HSA-69242 S Phase
R-HSA-162582 Signal Transduction
R-HSA-212436 Generic Transcription Pathway
R-HSA-69002 DNA Replication Pre-Initiation
R-HSA-69239 Synthesis of DNA
R-HSA-69613 p53-Independent G1/S DNA damage checkpoint
R-HSA-176814 Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-162906 HIV Infection
R-HSA-449147 Signaling by Interleukins
R-HSA-109581 Apoptosis
R-HSA-69563 p53-Dependent G1 DNA Damage Response
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-8953854 Metabolism of RNA
R-HSA-1280218 Adaptive Immune System
R-HSA-983705 Signaling by the B Cell Receptor (BCR)
R-HSA-2262749 Cellular response to hypoxia
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-168249 Innate Immune System
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-168256 Immune System
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-1640170 Cell Cycle
R-HSA-453274 Mitotic G2-G2/M phases
R-HSA-5619115 Disorders of transmembrane transporters
R-HSA-422475 Axon guidance
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-453279 Mitotic G1-G1/S phases
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-68874 M/G1 Transition
R-HSA-69306 DNA Replication
R-HSA-69615 G1/S DNA Damage Checkpoints
R-HSA-68886 M Phase
R-HSA-5663205 Infectious disease
R-HSA-5357801 Programmed Cell Death
R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint
R-HSA-1430728 Metabolism
R-HSA-2262752 Cellular responses to stress
R-HSA-1643685 Disease
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-1266738 Developmental Biology
R-HSA-74160 Gene expression (Transcription)
R-HSA-8953897 Cellular responses to external stimuli

-  Other Names for This Gene
  Alternate Gene Symbols: DSS1, DSS1_HUMAN, NM_006304, NP_006295, P60896, Q13437, Q61067, SHFDG1
UCSC ID: uc003uoi.3
RefSeq Accession: NM_006304
Protein: P60896 (aka DSS1_HUMAN)
CCDS: CCDS5646.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006304.1
exon count: 3CDS single in 3' UTR: no RNA size: 509
ORF size: 213CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 578.00frame shift in genome: no % Coverage: 97.84
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.