Tvp23a (trans-golgi network vesicle protein 23 homolog A) - Rat Genome Database

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Gene: Tvp23a (trans-golgi network vesicle protein 23 homolog A) Rattus norvegicus
Analyze
Symbol: Tvp23a
Name: trans-golgi network vesicle protein 23 homolog A
RGD ID: 1566405
Description: Predicted to be involved in protein secretion and vesicle-mediated transport. Predicted to be located in membrane. Predicted to be active in Golgi membrane. Orthologous to human TVP23A (trans-golgi network vesicle protein 23 homolog A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Fam18a; family with sequence similarity 18, member A; Golgi apparatus membrane protein TVP23 homolog A; hypothetical protein LOC360467; LOC360467; RGD1566405; similar to RIKEN cDNA 1810036I24; trans-golgi network vesicle protein 23 homolog A (S. cerevisiae); trans-golgi network vesicle protein 23A; uncharacterized protein LOC360467
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,734,100 - 5,770,002 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl105,734,100 - 5,769,998 (+)EnsemblGRCr8
mRatBN7.2105,227,198 - 5,263,185 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl105,227,220 - 5,263,180 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx109,923,605 - 9,959,515 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,444,724 - 9,480,628 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0105,082,998 - 5,118,997 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,300,319 - 5,335,160 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,300,384 - 5,334,262 (+)Ensemblrn6Rnor6.0
Rnor_5.0104,123,373 - 4,157,228 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4105,173,466 - 5,207,518 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera104,244,916 - 4,277,756 (+)NCBICelera
Cytogenetic Map10q11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Tvp23a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8105,734,100 - 5,770,002 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl105,734,100 - 5,769,998 (+)EnsemblGRCr8
mRatBN7.2105,227,198 - 5,263,185 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl105,227,220 - 5,263,180 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx109,923,605 - 9,959,515 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0109,444,724 - 9,480,628 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0105,082,998 - 5,118,997 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0105,300,319 - 5,335,160 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl105,300,384 - 5,334,262 (+)Ensemblrn6Rnor6.0
Rnor_5.0104,123,373 - 4,157,228 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4105,173,466 - 5,207,518 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera104,244,916 - 4,277,756 (+)NCBICelera
Cytogenetic Map10q11NCBI
TVP23A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381610,757,318 - 10,818,794 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1610,760,919 - 10,818,794 (-)Ensemblhg38GRCh38
GRCh371610,854,769 - 10,912,651 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361610,768,034 - 10,820,122 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1611,029,800 - 11,081,859 (-)NCBICelera
Cytogenetic Map16p13.13NCBI
HuRef1610,778,913 - 10,831,205 (-)NCBIHuRef
CHM1_11610,860,532 - 10,912,605 (-)NCBICHM1_1
T2T-CHM13v2.01610,796,831 - 10,854,673 (-)NCBIT2T-CHM13v2.0
Tvp23a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391610,237,397 - 10,265,251 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1610,238,421 - 10,265,226 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381610,419,533 - 10,447,390 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1610,420,557 - 10,447,362 (-)Ensemblmm10GRCm38
MGSCv371610,420,650 - 10,447,443 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361610,334,135 - 10,360,928 (-)NCBIMGSCv36mm8
Celera1611,054,067 - 11,080,863 (-)NCBICelera
Cytogenetic Map16A1NCBI
cM Map165.61NCBI
Tvp23a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554427,692,579 - 7,716,699 (+)Ensembl
ChiLan1.0NW_0049554427,691,770 - 7,716,383 (+)NCBIChiLan1.0ChiLan1.0
TVP23A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21811,298,287 - 11,365,049 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11615,069,694 - 15,140,633 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0169,689,717 - 9,757,842 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11610,926,248 - 10,980,351 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1610,932,704 - 10,980,351 (-)EnsemblpanPan2panpan1.1
TVP23A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1631,870,930 - 31,901,575 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl631,870,719 - 31,900,838 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha633,253,469 - 33,285,298 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0632,053,571 - 32,085,342 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl632,053,586 - 32,083,270 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1631,867,624 - 31,899,370 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0631,741,392 - 31,773,198 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0632,165,686 - 32,197,437 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tvp23a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344111,139,317 - 111,160,176 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365308,986,664 - 9,005,016 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365308,985,774 - 9,005,366 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TVP23A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl332,271,848 - 32,312,779 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1332,275,481 - 32,318,598 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2333,007,340 - 33,045,135 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TVP23A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl510,247,611 - 10,296,854 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606819,871,896 - 19,928,611 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tvp23a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248248,039,812 - 8,063,242 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248248,038,613 - 8,063,594 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tvp23a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1911,909,597 - 11,944,755 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tvp23a
262 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:339
Count of miRNA genes:208
Interacting mature miRNAs:257
Transcripts:ENSRNOT00000029359
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
1549898Neuinf3Neuroinflammation QTL 326.4nervous system integrity trait (VT:0010566)MHC Class II RT1A-positive spinal cord ventral horn area to total spinal cord ventral horn area ratio (CMO:0001980)1015893911Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 35 161 91 90 59 75 59 6 302 143 11 140 76 89 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001393687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245717 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245725 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006245726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597356 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597357 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597359 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597360 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597362 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC103514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ076704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ211935 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000029359   ⟹   ENSRNOP00000035280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl105,227,220 - 5,263,180 (+)Ensembl
Rnor_6.0 Ensembl105,300,384 - 5,334,262 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000145927   ⟹   ENSRNOP00000110455
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl105,734,100 - 5,769,998 (+)Ensembl
RefSeq Acc Id: NM_001108263   ⟹   NP_001101733
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,734,100 - 5,770,002 (+)NCBI
mRatBN7.2105,227,198 - 5,263,185 (+)NCBI
Rnor_6.0105,300,384 - 5,334,262 (+)NCBI
Rnor_5.0104,123,373 - 4,157,228 (+)NCBI
RGSC_v3.4105,173,466 - 5,207,518 (+)RGD
Celera104,244,916 - 4,277,756 (+)RGD
Sequence:
RefSeq Acc Id: NM_001393687   ⟹   NP_001380616
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8105,734,100 - 5,770,002 (+)NCBI
mRatBN7.2105,227,198 - 5,263,185 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101733 (Get FASTA)   NCBI Sequence Viewer  
  NP_001380616 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96222 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000110455
  ENSRNOP00000110455.1
RefSeq Acc Id: NP_001101733   ⟸   NM_001108263
- Peptide Label: isoform 1
- UniProtKB: A6K4K0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000035280   ⟸   ENSRNOT00000029359
RefSeq Acc Id: NP_001380616   ⟸   NM_001393687
- Peptide Label: isoform 2
Ensembl Acc Id: ENSRNOP00000110455   ⟸   ENSRNOT00000145927

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A2T2-F1-model_v2 AlphaFold D4A2T2 1-222 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566405 AgrOrtholog
BioCyc Gene G2FUF-26132 BioCyc
Ensembl Genes ENSRNOG00000025545 Ensembl
  ENSRNOG00000079813 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000145927 ENTREZGENE
  ENSRNOT00000145927.1 UniProtKB/TrEMBL
InterPro DUF846_euk UniProtKB/TrEMBL
KEGG Report rno:360467 UniProtKB/TrEMBL
NCBI Gene 360467 ENTREZGENE
PANTHER DUF846_euk UniProtKB/TrEMBL
  GOLGI APPARATUS MEMBRANE PROTEIN TVP23 HOMOLOG A UniProtKB/TrEMBL
Pfam DUF846 UniProtKB/TrEMBL
PhenoGen Tvp23a PhenoGen
RatGTEx ENSRNOG00000025545 RatGTEx
  ENSRNOG00000079813 RatGTEx
UniProt A0ABK0M668_RAT UniProtKB/TrEMBL
  A6K4K0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-19 Tvp23a  trans-golgi network vesicle protein 23 homolog A  Tvp23a  trans-golgi network vesicle protein 23A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-13 Tvp23a  trans-golgi network vesicle protein 23A  Tvp23a  trans-golgi network vesicle protein 23 homolog A (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-12-10 Tvp23a  trans-golgi network vesicle protein 23 homolog A (S. cerevisiae)  Fam18a  family with sequence similarity 18, member A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 Fam18a  family with sequence similarity 18, member A  RGD1566405  similar to RIKEN cDNA 1810036I24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566405  similar to RIKEN cDNA 1810036I24   RGD1566405_predicted  similar to RIKEN cDNA 1810036I24 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566405_predicted  similar to RIKEN cDNA 1810036I24 (predicted)  LOC360467  similar to RIKEN cDNA 1810036I24  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC360467  similar to RIKEN cDNA 1810036I24      Symbol and Name status set to provisional 70820 PROVISIONAL