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TVP23C-CDRT4 Gene

protein-coding   GIFtS: 19
GCID: GC17M015352

TVP23C-CDRT4 Readthrough

(Previous name: FAM18B2-CDRT4 readthrough)
(Previous symbol: FAM18B2-CDRT4)
  Search for TVP23C-CDRT4
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
TVP23C-CDRT4 Readthrough1 2     TVP23B4
FAM18B2-CDRT41 2     Golgi Apparatus Membrane Protein TVP23 Homolog C4
FAM18B2-CDRT4 Readthrough1 2     Protein TVP23C-CDRT44
Uncharacterized Protein LOC1005334962     

External Ids:    HGNC: 429611   Entrez Gene: 1005334962   Ensembl: ENSG000002590247   UniProtKB: E5RGC54   UniProtKB: E5RIS54   
ORGUL members:         

Export aliases for TVP23C-CDRT4 gene to outside databases

Previous GC identifers: GC17M015342 GC17M015345


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TVP23C-CDRT4 Gene:
This locus represents naturally occurring read-through transcription between the neighboring FAM18B2 (family with
sequence similarity 18, member B2) and CDRT4 (CMT1A duplicated region transcript 4) genes on chromosome 17.
Alternative splicing results in multiple transcript variants, one of which encodes a protein that shares sequence
identity with the upstream gene product, but its C-terminus is distinct due to frameshifts relative to the
downstream gene. (provided by RefSeq, Mar 2011)

GeneCards Summary for TVP23C-CDRT4 Gene:
TVP23C-CDRT4 (TVP23C-CDRT4 readthrough) is a protein-coding gene. An important paralog of this gene is TVP23B.




(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for TVP23C-CDRT4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TVP23C-CDRT4


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

Entrez Gene cytogenetic band: 17p   Ensembl cytogenetic band:  17p12   HGNC cytogenetic band: 17p12

TVP23C-CDRT4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TVP23C-CDRT4 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M015352:  view genomic region     (about GC identifiers)

Start:
15,339,332 bp from pter      End:
15,466,945 bp from pter
Size:
127,614 bases      Orientation:
minus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/TrEMBL: E5RGC5 (See protein sequence)
Recommended Name: Golgi apparatus membrane protein TVP23 homolog C  
Size: 53 amino acids; 6152 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: E5RIS5 (See protein sequence)

Recommended Name: Golgi apparatus membrane protein TVP23 homolog B  
Size: 37 amino acids; 4314 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data
Secondary accessions: D6R9A3

REFSEQ proteins: NP_001191407.1  
ENSEMBL proteins: 
 ENSP00000429865   ENSP00000450826   ENSP00000423249   ENSP00000430143  

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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:
 IPR008564 DUF846_euk

Graphical View of Domain Structure for InterPro Entry E5RGC5
Graphical View of Domain Structure for InterPro Entry E5RIS5

ProtoNet protein and cluster: E5RGC5


TVP23C-CDRT4 for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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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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Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral component of membrane ----

TVP23C-CDRT4 for ontologies           About GeneDecksing


(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 TVP23C-CDRT4
Interactions:

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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
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Browse Tocris compounds for TVP23C-CDRT4



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for TVP23C-CDRT4 gene: 
NM_001204478.1  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000522212(uc010vvx.2 uc021tqm.1 uc010vvw.2) ENST00000557349
ENST00000481756 ENST00000518506
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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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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

TVP23C-CDRT4 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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(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 animals and fungi.

Orthologs for TVP23C-CDRT4 gene from Selected species (see all 10)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
oppossum
(Monodelphis domestica)
Mammalia --
Uncharacterized protein
64(a)
1 → many
2(262590083-262675060)
chicken
(Gallus gallus)
Aves FAM18B16
Gallus gallus family with sequence similarity 18, ...
59(a)
1 → many
18(2223389-2230202)
lizard
(Anolis carolinensis)
Reptilia --
Golgi apparatus membrane protein TVP23 homolog B (...
62(a)
1 → many
2(106172688-106179413)
zebrafish
(Danio rerio)
Actinopterygii tvp23b6
zgc:1121486
zgc:112148
52(a)
47(a)
many ↔ many
many ↔ many
12(47758081-47770806) ENSDARG00000057060
3(57615700-57625918) ENSDARG00000001804
fruit fly
(Drosophila melanogaster)
Insecta CG50216
--
32(a)
1 → many
3L(8959929-8961271)
worm
(Caenorhabditis elegans)
Secernentea C34D4.46
Protein C34D4.4, isoform a
21(a)
1 → many
IV(7149337-7150690) WBGene00016400
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TVP236
Integral membrane protein localized to late Golgi ...
20(a)
1 → many
IV(613405-614004) YDR084C


ENSEMBL Gene Tree for TVP23C-CDRT4 (if available)
TreeFam Gene Tree for TVP23C-CDRT4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TVP23C-CDRT4 gene
TVP23B2  TVP23C2  TVP23A2  

TVP23C-CDRT4 for paralogs           About GeneDecksing



(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 TVP23C-CDRT4 (see all 2010)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs65024511,2
C,F,A,H--15360344(+) GCTGCT/CTGGTA 2 -- int19Minor allele frequency- C:0.07NS EA NA CSA WA 610
rs1929117351,2
--15360375(+) TAAGTC/GCAGCC 2 -- int10--------
rs72126141,2
C,F,A,H--15360446(+) CACCCA/GTGCAC 2 -- int120Minor allele frequency- G:0.07NS EA NA CSA WA 2342
rs1409732141,2
--15360521(+) CAGGAA/GTACCT 2 -- int10--------
rs1497780191,2
--15360612(+) ATACAC/GAATTC 2 -- int10--------
rs728244571,2
C--15360690(+) TCCCCA/GCCTGA 2 -- int12Minor allele frequency- G:0.13NA 122
rs1849479941,2
--15360751(+) CAACTC/TACATT 2 -- int10--------
rs1153310891,2
C,F--15360830(+) CTCCAC/TGCTCA 2 -- int11Minor allele frequency- T:0.02WA 118
rs1467732561,2
--15360831(+) TCCACA/GCTCAA 2 -- int10--------
rs2015926721,2
--15360878(+) CAATG-/CTCGTTA 2 -- int10--------

HapMap Linkage Disequilibrium report for TVP23C-CDRT4 (15339332 - 15466945 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TVP23C-CDRT4: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing TVP23C-CDRT4
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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  --

(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 TVP23C-CDRT4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TVP23C-CDRT4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
  2. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262)1 Prakash T....Taylor T.D. (PLoS ONE 2010)
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  4. 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: 100533496 HGNC: 42961 Ensembl:ENSG00000259024 euGenes: HUgn100533496 ECgene: TVP23C-CDRT4
H-InvDB: TVP23C-CDRT4

(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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  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for TVP23C-CDRT4 gene:
Search GeneIP for patents involving TVP23C-CDRT4

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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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

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The GeneCards human gene database gene index: 1 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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