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C8orf48 Gene

protein-coding   GIFtS: 43
GCID: GC08P013469

Chromosome 8 Open Reading Frame 48

  Search for C8orf48
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chromosome 8 Open Reading Frame 481 2
Uncharacterized Protein C8orf482

External Ids:    HGNC: 263451   Entrez Gene: 1577732   Ensembl: ENSG000001647437   UniProtKB: Q96LL43   

Export aliases for C8orf48 gene to outside databases

Previous GC identifer: GC08P011966


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for C8orf48 Gene:
C8orf48 (chromosome 8 open reading frame 48) is a protein-coding gene.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000008.10  NC_018919.2  NT_167187.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the C8orf48 gene promoter:
         C/EBPbeta   USF1   Tal-1   AML1a   Cdc5   RORalpha2   AREB6   USF-1   Sox9   Chx10   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C8orf48

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C8orf48


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 8p22   Ensembl cytogenetic band:  8p22   HGNC cytogenetic band: 8p22

C8orf48 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C8orf48 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P013469:  view genomic region     (about GC identifiers)

Start:
13,424,352 bp from pter      End:
13,425,797 bp from pter
Size:
1,446 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CH048_HUMAN, Q96LL4 (See protein sequence)
Recommended Name: Uncharacterized protein C8orf48  
Size: 319 amino acids; 36790 Da
Sequence caution: Sequence=BAB71692.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: Q96LJ9

Explore the universe of human proteins at neXtProt for C8orf48: NX_Q96LL4

Explore proteomics data for C8orf48 at MOPED


See C8orf48 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001007091.1  
ENSEMBL proteins: 
 ENSP00000297324  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR027932 DUF4606

Graphical View of Domain Structure for InterPro Entry Q96LL4

ProtoNet protein and cluster: Q96LL4


Find genes that share domains with C8orf48           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI16189514
     
Find genes that share ontologies with C8orf48           About GenesLikeMe


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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus3
cytosol2

(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for C8orf48
Interactions:

    Search GeneGlobe Interaction Network for C8orf48

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for C8orf48 (Q96LL41, 2, 3 ENSP000002973244) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
CCDC85BQ158342, 3, ENSP000003116954MINT-68266 I2D: score=4 STRING: ENSP00000311695
MDFIQ997501, 2, 3, ENSP000002303214EBI-751596,EBI-724076 MINT-68178 I2D: score=4 STRING: ENSP00000230321
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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for C8orf48 (CH048)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for C8orf48 gene: 
NM_001007090.2  

Unigene Cluster for C8orf48:

Chromosome 8 open reading frame 48
Hs.104941  [show with all ESTs]
Unigene Representative Sequence: NM_001007090
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000297324(uc003wwp.3)
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat C8orf48

Additional mRNA sequence: 

AF394908.1 AK058131.1 AK058156.1 BC031245.1 

2 DOTS entries:

DT.101971458  DT.307297 

22 AceView cDNA sequences:

AA992956 BQ575896 BI459420 AK058131 CA428557 AK058156 BQ429960 CB113670 
BX095759 BC031245 AA496024 BU625852 CB306127 CK128686 AA436936 AI150511 
BQ575707 AI205913 AW337731 BP370159 BE567861 W69991 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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C8orf48 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: AAGATAAATT
C8orf48 Expression
About this image


C8orf48 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 5) fully expand
 
 Brain (Nervous System)    fully expand to see all 3 entries
         Cerebral Cortex
 
 Trophoblast (Extraembryonic Tissues)
         Trophoblast Cells Trophoblast
 
 Ovary (Reproductive System)
         Oviduct
 
 Testis (Reproductive System)
         Leydig Cells Testis Interstitium
 
 Bone (Muscoskeletal System)
         Bone Marrow
C8orf48 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C8orf48 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.104941
    Custom PCR Arrays for C8orf48
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C8orf48

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for C8orf48 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia AI4292141 , 5 expressed sequence AI4292141, 5 72.65(n)1
60.26(a)1
  8 (23.15 cM)5
6210801  NM_001039220.31  NP_001034309.11 
 369935755 
chicken
(Gallus gallus)
Aves LOC7717521 uncharacterized LOC771752 61.08(n)
41.38(a)
  771752  XM_001234996.3  XP_001234997.3 
lizard
(Anolis carolinensis)
Reptilia C8orf486
chromosome 8 open reading frame 48
45(a)
1 ↔ 1
GL343376.1(844372-848916)


ENSEMBL Gene Tree for C8orf48 (if available)
TreeFam Gene Tree for C8orf48 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for C8orf48 (see all 114)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 8 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1874208211,2
--13679263(+) ACTCTC/TTTTTC 1 -- us2k10--------
rs178234991,2
C,F--13679328(+) CCACAA/CAGCAT 1 -- us2k16Minor allele frequency- C:0.07NA WA EA 486
rs1478133951,2
--13679415(+) TGTTTA/TAAATC 1 -- us2k10--------
rs1413237191,2
C--13679538(+) CTGAAC/TATTAC 1 -- us2k10--------
rs1499432491,2
--13679579(+) CATATA/GTCTCC 1 -- us2k10--------
rs624921361,2
C--13679583(+) TATCTC/GCTTCT 1 -- us2k13Minor allele frequency- G:0.08NA EA 242
rs69840111,2
C,F,A,H--13679631(+) GACACT/GATTAT 1 -- us2k115Minor allele frequency- G:0.14NS EA NA WA CSA 791
rs1905917721,2
--13679806(+) AATAAC/TAAATA 1 -- us2k10--------
rs781284491,2
F--13679859(+) ACAAAT/CTACAT 1 -- us2k11Minor allele frequency- C:0.03EA 120
rs1452353731,2
--13679912(+) ATTTGG/TGTTGA 1 -- us2k10--------

HapMap Linkage Disequilibrium report for C8orf48 (13424352 - 13425797 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for C8orf48:    About this table    
Variant IDTypeSubtypePubMed ID
nsv470185CNV Loss18288195
nsv890395CNV Gain21882294
nsv890394CNV Gain21882294
nsv890396CNV Gain21882294
nsv8290CNV Gain18304495
nsv517019CNV Gain+Loss19592680

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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Find genes that share disorders with C8orf48           About GenesLikeMe

Genetic Association Database (GAD): C8orf48

Export disorders for C8orf48 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for C8orf48 gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with C8orf48)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  2. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (Nat. Methods 2013)
  3. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  4. An empirical framework for binary interactome mapping. (PubMed id 19060904)1 Venkatesan K....Vidal M. (Nat. Methods 2009)
  5. Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study. (PubMed id 17903303)4 O'Donnell C.J....Demissie S. (BMC Med. Genet. 2007)
  6. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (Nature 2006)
  7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  10. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 157773 HGNC: 26345 AceView: FLJ25402 Ensembl:ENSG00000164743 euGenes: HUgn157773
ECgene: C8orf48 H-InvDB: C8orf48

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for C8orf48 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for C8orf48 gene:
Search GeneIP for patents involving C8orf48

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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