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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TVP23C-CDRT4 Gene

protein-coding   GIFtS: 20
GCID: GC17M015345

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)
About This Section

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:         
NONCODE14:n410674      

Export aliases for TVP23C-CDRT4 gene to outside databases

Previous GC identifer: GC17M015342


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and is affiliated with the lncRNA class. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for TVP23C-CDRT4
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 GC17M015345:  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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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

TVP23C-CDRT4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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

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Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016021integral to membrane ----

TVP23C-CDRT4 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TVP23C-CDRT4

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Browse Tocris compounds for TVP23C-CDRT4

Search CenterWatch for drugs/clinical trials and news about 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,
RNAi Products from EMD Millipore,
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About This Section

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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

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In Situ
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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)
About This Section

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

Orthologs for TVP23C-CDRT4 gene from 6/13 species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves TVP23B6
uncharacterized protein LOC417324
59(a)
1 → many
18(2223389-2230202)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
62(a)
1 → many
2(106172688-106179413)
zebrafish
(Danio rerio)
Actinopterygii tvp23b6
zgc:1121486
zgc:112148
50(a)
48(a)
many ↔ many
many ↔ many
12(47758183-47771010)
3(57615700-57625915)
fruit fly
(Drosophila melanogaster)
Insecta CG50216
--
32(a)
1 → many
3L(8959929-8961271)
worm
(Caenorhabditis elegans)
Secernentea C34D4.46
Uncharacterized FAM18-like protein C34D4.4
21(a)
1 → many
IV(7149337-7150690)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TVP236
Integral membrane protein localized to late Golgi ...
19(a)
1 → many
IV(613405-614004)
        Species with no ortholog for TVP23C-CDRT4

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)
About This Section
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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/2010 SNPs in TVP23C-CDRT4 are shown (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: --
SABiosciences Cancer Mutation PCR Assays
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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.)
About This Section
  --

(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)
About This Section

PubMed articles for TVP23C-CDRT4 gene integrated from 9 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 ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
  2. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262)1 Prakash T....Taylor T.D. (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. (2006)
  4. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 100533496 HGNC: 42961 Ensembl:ENSG00000259024 euGenes: HUgn100533496 ECgene: TVP23C-CDRT4
H-InvDB: TVP23C-CDRT4

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
  --

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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About This Section

 
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 Codon Optimization
 Protein Production and Purification
 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TVP23C-CDRT4
 Browse SwitchGear 3'UTR luciferase reporter plasmids for TVP23C-CDRT4
 Browse SwitchGear Promoter luciferase reporter plasmids for TVP23C-CDRT4
 Search ThermoFisher Antibodies for TVP23C-CDRT4
 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat TVP23C-CDRT4
 inGenious Targeting Laboratory - Custom generated mouse model solutions for TVP23C-CDRT4
 inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for TVP23C-CDRT4
Customized:
 lentivirus for stable overexpression of TVP23C-CDRT4
 lentivirus expression plasmids for stable overexpression of TVP23C-CDRT4
 adenovirus for overexpression of TVP23C-CDRT4
 Search LSBio for Antibodies for TVP23C-CDRT4
Customized transgenic rodents for:
 Humanization
 Biomarker expression
 Off-target effect monitoring
 Translational medicine
 Tissue-specific gene expresssion
 Time-controlled gene expresssion
       
GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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