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TVP23A Gene

protein-coding   GIFtS: 34
GCID: GC16M010873

Trans-Golgi Network Vesicle Protein 23 Homolog A (S. Cerevisiae)

(Previous names: family with sequence similarity 18, member A)
(Previous symbol: FAM18A)
  See related diseases
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
Trans-Golgi Network Vesicle Protein 23 Homolog A (S. Cerevisiae)1 2
FAM18A1 2 3
Family With Sequence Similarity 18, Member A1 2
YDR084C2
Golgi Apparatus Membrane Protein TVP23 Homolog A2
Protein FAM18A2

External Ids:    HGNC: 203981   Entrez Gene: 7807762   Ensembl: ENSG000001666767   UniProtKB: A6NH523   
ORGUL members:         

Export aliases for TVP23A gene to outside databases

Previous GC identifers: GC16M010856 GC16M010864


(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 TVP23A Gene:
TVP23A (trans-golgi network vesicle protein 23 homolog A (S. cerevisiae)) is a protein-coding gene. Diseases associated with TVP23A include malaria, and neuronitis. An important paralog of this gene is TVP23C-CDRT4.


(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:
NC_000016.10  NT_010393.17  NC_018927.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TVP23A
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for TVP23A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TVP23A


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

Entrez Gene cytogenetic band: 16p13.13   Ensembl cytogenetic band:  16p13.13   HGNC cytogenetic band: 16p13.3

TVP23A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TVP23A gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M010873:  view genomic region     (about GC identifiers)

Start:
10,854,776 bp from pter      End:
10,912,651 bp from pter
Size:
57,876 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TV23A_HUMAN, A6NH52 (See protein sequence)
Recommended Name: Golgi apparatus membrane protein TVP23 homolog A  
Size: 213 amino acids; 24111 Da
Secondary accessions: B2RUV4

Explore the universe of human proteins at neXtProt for TVP23A: NX_A6NH52

Explore proteomics data for TVP23A at MOPED


See TVP23A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001072980.1  
ENSEMBL proteins: 
 ENSP00000460567   ENSP00000411972   ENSP00000460822   ENSP00000458488   ENSP00000299866  
 ENSP00000461067  

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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 A6NH52

ProtoNet protein and cluster: A6NH52

UniProtKB/Swiss-Prot: TV23A_HUMAN, A6NH52
Similarity: Belongs to the TVP23 family


TVP23A 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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Phenotypes:
     1 GenomeRNAi human phenotype for TVP23A:
 Decreased TP53 protein express 

Animal Models:
   inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TVP23A
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miRNA
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miRTarBase miRNAs that target TVP23A:
hsa-mir-335-5p (MIRT017198)

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TVP23A


(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 UniProtKB/Swiss-Prot
TV23A_HUMAN, A6NH52: Membrane; Multi-pass membrane protein (Potential)

Gene Ontology (GO): 1 cellular component term:    About this table

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

TVP23A 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 TVP23A
Interactions:

    Search GeneGlobe Interaction Network for TVP23A

STRING Interaction Network Preview (showing 5 interactants - click image to see 23)

Selected Interacting proteins for TVP23A (ENSP000002998664) via UniProtKB, MINT, STRING, and/or I2D (see all 23)
InteractantInteraction Details
GeneCardExternal ID(s)
YIPF6ENSP000004175734STRING: ENSP00000417573
APRTENSP000003676154STRING: ENSP00000367615
VTI1AENSP000003767924STRING: ENSP00000376792
STX10ENSP000002427704STRING: ENSP00000242770
STX6ENSP000002583014STRING: ENSP00000258301
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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 TVP23A (TV23A)



(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 TVP23A gene: 
NM_001079512.2  

Unigene Cluster for TVP23A:

Trans-golgi network vesicle protein 23 homolog A (S. cerevisiae)
Hs.371576  [show with all ESTs]
Unigene Representative Sequence: AK124106
9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000572980(uc002dad.3) ENST00000573857(uc010uyr.1) ENST00000575135(uc010uyt.1 uc010bun.2)
ENST00000456096(uc010uys.1 uc010uyu.1) ENST00000572428(uc002dae.1)
ENST00000573360(uc002daf.1) ENST00000299866(uc010buo.1) ENST00000572102
ENST00000570692
miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat TVP23A

Additional mRNA sequence: 

AK124106.1 AK294418.1 AL833564.1 BC050569.1 BC146882.1 BC146886.1 BC171807.1 BC171816.1 
BC171817.1 BC171819.1 

6 DOTS entries:

DT.101979088  DT.75160830  DT.100785305  DT.95226532  DT.100785307  DT.444422 

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for TVP23A    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7a · 7b
SP1:                                            -     -                                       
SP2:                                -     -     -     -                                       
SP3:                                -                                                         
SP4:                                -     -                                                   
SP5:                                                                                          


ECgene alternative splicing isoforms for TVP23A

(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: --


TVP23A expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 3) fully expand
 
 Neurons
         AII Amacrine Cells Inner Nuclear Layer
 
 Eye (Sensory Organs)
         AII Amacrine Cells Inner Nuclear Layer
 
 Spinal Cord (Nervous System)
TVP23A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TVP23A Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.371576
    Custom PCR Arrays for TVP23A
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TVP23A

(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 eukaryotes.

Orthologs for TVP23A gene from Selected species (see all 20)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Tvp23a1 , 5 family with sequence similarity 18, member A5
trans-golgi network vesicle protein 23A1
84.98(n)1
88.26(a)1
  16 (5.61 cM)5
3831031  NM_001013778.11  NP_001013800.11 
 104205575 
chicken
(Gallus gallus)
Aves FAM18A1 family with sequence similarity 18, member A 73.01(n)
77.07(a)
  771988  XM_001234549.3  XP_001234550.2 
tropical clawed frog
(Xenopus tropicalis)
Amphibia tvp23a1 trans-golgi network vesicle protein 23 homolog A (S. more 73.12(n)
77.49(a)
  100489165  XM_002939187.1  XP_002939233.1 
fruit fly
(Drosophila melanogaster)
Insecta CG50211 CG5021 57.26(n)
50.26(a)
  39025  NM_001169920.2  NP_001163391.1 
worm
(Caenorhabditis elegans)
Secernentea C34D4.46
Protein C34D4.4, isoform a
26(a)
1 → many
IV(7149337-7150690) WBGene00016400
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TVP231 TVP23 44(n)
38.67(a)
  851657   NP_010369.3 
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G093301 AT1G09330 48.37(n)
38.41(a)
  837454  NM_100803.3  NP_563842.1 
rice
(Oryza sativa)
Liliopsida Os01g03319001 Os01g0331900 46.91(n)
37.72(a)
  4326837  NM_001049465.1  NP_001042930.1 


ENSEMBL Gene Tree for TVP23A (if available)
TreeFam Gene Tree for TVP23A (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TVP23A gene
TVP23C-CDRT42  TVP23B2  TVP23C2  
3 SIMAP similar genes for TVP23A using alignment to 5 protein entries:     TV23A_HUMAN (see all proteins):
FAM18B2    TVP23B    TVP23C

TVP23A 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 TVP23A (see all 1322)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs616938511,2
C,F--10863745(+) TGGGAG/AAAGAG 1 -- int13Minor allele frequency- A:0.29WA CSA 122
rs1899666751,2
--10863821(+) CCTTGC/TTCTTT 1 -- int10--------
rs744493841,2
C,F--10863929(+) GACCCC/TCAGCT 1 -- int11Minor allele frequency- T:0.12NA 120
rs1151451991,2
F--10863958(+) GAGGCT/CGCAAA 1 -- int11Minor allele frequency- C:0.02WA 118
rs1501957531,2
--10864158(+) CTCGAA/GGCCAG 2 L F mis10--------
rs1387459831,2
C--10864165(+) CCAGGA/CTTCTG 2 K N mis10--------
rs169576471,2
C--10864210(+) CAACCA/GTGGTT 1 -- int13Minor allele frequency- G:0.01NA 140
rs1812634551,2
C--10864213(+) CCATGA/GTTTTC 1 -- int10--------
rs1998703531,2
--10864234(+) CGCGAC/GTGGGG 1 -- int10--------
rs1849242801,2
--10864273(+) ACCCAA/CAAAGT 1 -- int10--------

HapMap Linkage Disequilibrium report for TVP23A (10854776 - 10912651 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for TVP23A: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing TVP23A
DNA2.0 Custom Variant and Variant Library Synthesis for TVP23A

(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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2 diseases for TVP23A:    
About MalaCards
malaria    neuronitis


TVP23A for disorders           About GeneDecksing


Export disorders for TVP23A 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 TVP23A gene integrated from 10 sources:
(articles sorted by number of sources associating them with TVP23A)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)2 Martin J.... Pennacchio L.A. (Nature 2004)
  2. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (Nat. Biotechnol. 2004)
  3. 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)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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: 780776 HGNC: 20398 Ensembl:ENSG00000166676 euGenes: HUgn780776 ECgene: TVP23A
H-InvDB: TVP23A

(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 TVP23A 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 TVP23A gene:
Search GeneIP for patents involving TVP23A

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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Block miRNA regulation of human, mouse, rat TVP23A using miScript Target Protectors SeqTarget long-range PCR primers for resequencing TVP23A
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 Custom PCR Arrays for TVP23A Search Chromatin IP Primers for TVP23A
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 GenScript Custom Purified and Recombinant Proteins Services for TVP23A GenScript Custom cDNA clones with any tag delivered in your preferred vector Services for TVP23A
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 Search Tocris compounds for TVP23A (TV23A)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

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 Search for Antibodies for TVP23A at Abcam
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 Browse ESI BIO Cell Lines and PureStem Progenitors for TVP23A
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 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for TVP23A
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 Search LSBio for Antibodies for TVP23A
Customized transgenic rodents for:
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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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