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Aliases for MSH5-SAPCD1 Gene

Subcategory (RNA class) for MSH5-SAPCD1 Gene

ncRNA

Quality Score for this RNA gene is

3

Aliases for MSH5-SAPCD1 Gene

  • MSH5-SAPCD1 Readthrough (NMD Candidate) 2 3 5
  • MSH5-C6orf26 Readthrough (Non-Protein Coding) 2 3
  • MSH5-SAPCD1 Readthrough (Non-Protein Coding) 3
  • MSH5-C6orf26 3

External Ids for MSH5-SAPCD1 Gene

Previous HGNC Symbols for MSH5-SAPCD1 Gene

  • MSH5-C6orf26

Previous GeneCards Identifiers for MSH5-SAPCD1 Gene

  • GC06P031708
  • GC06P031714
  • GC06P031729
  • GC06P031764
  • GC06P031766
  • GC06P031839

Summaries for MSH5-SAPCD1 Gene

Entrez Gene Summary for MSH5-SAPCD1 Gene

  • This locus represents naturally occurring read-through transcription between the neighboring mutS homolog 5 (MSH5) and chromosome 6 open reading frame 26 (C6orf26) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. [provided by RefSeq, Feb 2011]

GeneCards Summary for MSH5-SAPCD1 Gene

MSH5-SAPCD1 (MSH5-SAPCD1 Readthrough (NMD Candidate)) is an RNA Gene, and is affiliated with the ncRNA class. GO annotations related to this gene include mismatched DNA binding. An important paralog of this gene is MSH5.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MSH5-SAPCD1 Gene

Genomics for MSH5-SAPCD1 Gene

Regulatory Elements for MSH5-SAPCD1 Gene

Enhancers for MSH5-SAPCD1 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
GH06F031710 0.5 Ensembl 11.8 -28.4 -28448 2.2 YBX3 HDGF CTCF KLF1 ESRRA ETV1 KLF17 CDC5L RAD21 ZIC2 LY6G5C SKIV2L MSH5 MSH5-SAPCD1 SAPCD1 SAPCD1-AS1 VWA7 RNU6-850P ENSG00000201555 VARS
GH06F031829 0.2 ENCODE 11.6 +94.2 94209 9.1 CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 MEF2D GLIS1 ATF6B LSM2 LY6G5B DDX39B SKIV2L DXO GTF2H4 VARS LY6G6C CSNK2B
GH06F031805 0.7 ENCODE 11.5 +66.9 66853 2.0 HDGF PKNOX1 ARNT CREB3L1 MLX WRNIP1 ARID4B SIN3A DMAP1 ZNF2 LSM2 DXO ATF6B GTF2H4 RPL3P2 VWA7 ENSG00000201555 SAPCD1 SAPCD1-AS1 MSH5
GH06F031920 0.4 Ensembl 10.7 +181.0 180953 0.6 SOX13 CTCF ARID4B CEBPG RAD21 GATA3 ZNF143 SMC3 PRDM10 TCF7L2 SKIV2L MIR1236 STK19 C4A VWA7 SAPCD1 RNU6-850P MSH5 MSH5-SAPCD1 SAPCD1-AS1
GH06F031861 0.2 ENCODE 10.7 +124.2 124168 4.5 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF548 ZNF263 LY6G5B LSM2 MICA C4A SNORA38 ENSG00000233902 LOC102725019 DDX39B STK19B LY6G5C
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around MSH5-SAPCD1 on UCSC Golden Path with GeneCards custom track

Promoters for MSH5-SAPCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000487898 252 1601 HDGF PKNOX1 ARNT CREB3L1 MLX ZFP64 SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for MSH5-SAPCD1 Gene

Chromosome:
6
Start:
31,739,948 bp from pter
End:
31,764,851 bp from pter
Size:
24,904 bases
Orientation:
Plus strand

Genomic View for MSH5-SAPCD1 Gene

Genes around MSH5-SAPCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MSH5-SAPCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MSH5-SAPCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for MSH5-SAPCD1 Gene

  • Protein details for MSH5-SAPCD1 Gene (UniProtKB/TrEMBL)

    Protein Symbol:
    A0A024RCV8
    Recommended name:
    MutS homolog 5 (E. coli), isoform CRA_b
    Protein Accession:
    A0A024RCV8

    Protein attributes for MSH5-SAPCD1 Gene

    Size:
    851 amino acids
    Molecular mass:
    94719 Da
    Quaternary structure:
    No Data Available
  • Protein details for MSH5-SAPCD1 Gene (UniProtKB/TrEMBL)

    Protein Symbol:
    A0A0G2JJ70
    Recommended name:
    MutS protein homolog 5
    Protein Accession:
    A0A0G2JJ70

    Protein attributes for MSH5-SAPCD1 Gene

    Size:
    496 amino acids
    Molecular mass:
    54659 Da
    Quaternary structure:
    No Data Available
  • Protein details for MSH5-SAPCD1 Gene (UniProtKB/TrEMBL)

    Protein Symbol:
    H0YEB2
    Recommended name:
    Protein MSH5-SAPCD1
    Protein Accession:
    H0YEB2

    Protein attributes for MSH5-SAPCD1 Gene

    Size:
    29 amino acids
    Molecular mass:
    3229 Da
    Quaternary structure:
    No Data Available
  • Protein details for MSH5-SAPCD1 Gene (UniProtKB/TrEMBL)

    Protein Symbol:
    H0YF11
    Recommended name:
    Protein MSH5-SAPCD1
    Protein Accession:
    H0YF11

    Protein attributes for MSH5-SAPCD1 Gene

    Size:
    264 amino acids
    Molecular mass:
    28741 Da
    Quaternary structure:
    No Data Available

neXtProt entry for MSH5-SAPCD1 Gene

Post-translational modifications for MSH5-SAPCD1 Gene

No Post-translational modifications

Other Protein References for MSH5-SAPCD1 Gene

No data available for DME Specific Peptides for MSH5-SAPCD1 Gene

Domains & Families for MSH5-SAPCD1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with MSH5-SAPCD1: view

No data available for Gene Families , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for MSH5-SAPCD1 Gene

Function for MSH5-SAPCD1 Gene

Gene Ontology (GO) - Molecular Function for MSH5-SAPCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030983 mismatched DNA binding IEA --
genes like me logo Genes that share ontologies with MSH5-SAPCD1: view

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for MSH5-SAPCD1 Gene

Localization for MSH5-SAPCD1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for MSH5-SAPCD1 Gene

Pathways & Interactions for MSH5-SAPCD1 Gene

SuperPathways for MSH5-SAPCD1 Gene

No Data Available

Interacting Proteins for MSH5-SAPCD1 Gene

Gene Ontology (GO) - Biological Process for MSH5-SAPCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006298 mismatch repair IEA --
genes like me logo Genes that share ontologies with MSH5-SAPCD1: view

No data available for Pathways by source and SIGNOR curated interactions for MSH5-SAPCD1 Gene

Transcripts for MSH5-SAPCD1 Gene

mRNA/cDNA for MSH5-SAPCD1 Gene

(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for MSH5-SAPCD1 Gene

No ASD Table

Relevant External Links for MSH5-SAPCD1 Gene

GeneLoc Exon Structure for
MSH5-SAPCD1
ECgene alternative splicing isoforms for
MSH5-SAPCD1

Expression for MSH5-SAPCD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MSH5-SAPCD1 Gene

genes like me logo Genes that share expression patterns with MSH5-SAPCD1: view

No data available for 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 , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for MSH5-SAPCD1 Gene

Orthologs for MSH5-SAPCD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for MSH5-SAPCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 35
  • 99 (a)
OneToMany
cow
(Bos Taurus)
Mammalia MSH5 35
  • 93 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Msh5 35
  • 89 (a)
OneToMany
dog
(Canis familiaris)
Mammalia MSH5 35
  • 87 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 78 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 70 (a)
ManyToMany
-- 35
  • 64 (a)
ManyToMany
-- 35
  • 60 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 66 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii MSH5 35
  • 53 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea msh-5 35
  • 17 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MSH5 35
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 41 (a)
OneToMany
Species where no ortholog for MSH5-SAPCD1 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)
  • 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)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)

Evolution for MSH5-SAPCD1 Gene

ENSEMBL:
Gene Tree for MSH5-SAPCD1 (if available)
TreeFam:
Gene Tree for MSH5-SAPCD1 (if available)

Paralogs for MSH5-SAPCD1 Gene

Paralogs for MSH5-SAPCD1 Gene

(4) SIMAP similar genes for MSH5-SAPCD1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with MSH5-SAPCD1: view

Variants for MSH5-SAPCD1 Gene

Sequence variations from dbSNP and Humsavar for MSH5-SAPCD1 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1053736 -- 31,740,535(+) TCCGG(C/T)TTCCC nc-transcript-variant, upstream-variant-2KB, reference, synonymous-codon
rs111468971 -- 31,762,942(+) AGCAG(A/G)AAGGG nc-transcript-variant, downstream-variant-500B, upstream-variant-2KB
rs111831265 -- 31,757,135(+) TGTTT(-/TTTG)TTTGT intron-variant
rs112145890 -- 31,742,911(+) GTTAC(A/G)AGTGC nc-transcript-variant, reference, synonymous-codon
rs112147492 -- 31,759,989(+) AGAGG(C/T)GGGTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for MSH5-SAPCD1 Gene

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
esv2763547 CNV loss 21179565
esv3608568 CNV loss 21293372
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv819978 CNV loss 19587683

Relevant External Links for MSH5-SAPCD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MSH5-SAPCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MSH5-SAPCD1 Gene

Disorders for MSH5-SAPCD1 Gene

Relevant External Links for MSH5-SAPCD1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
MSH5-SAPCD1

No disorders were found for MSH5-SAPCD1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for MSH5-SAPCD1 Gene

Publications for MSH5-SAPCD1 Gene

  1. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PMID: 20967262) Prakash T. … Taylor T.D. (PLoS ONE 2010) 3 64
  2. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. (PMID: 18204446) Harley J.B. … Kelly J.A. (Nat. Genet. 2008) 3 64
  3. Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit (CSNK2B). (PMID: 8812450) Albertella M.R. … Campbell R.D. (Genomics 1996) 3 64
  4. Identification of multiple HTF-island associated genes in the human major histocompatibility complex class III region. (PMID: 2477242) Sargent C.A. … Campbell R.D. (EMBO J. 1989) 3 64

Products for MSH5-SAPCD1 Gene

Sources for MSH5-SAPCD1 Gene

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