Tnxa-ps1 (tenascin XA, pseudogene 1) - Rat Genome Database

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Gene: Tnxa-ps1 (tenascin XA, pseudogene 1) Rattus norvegicus
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Symbol: Tnxa-ps1
Name: tenascin XA, pseudogene 1
RGD ID: 3887
Description: Orthologous to human TNXA (tenascin XA (pseudogene)); INTERACTS WITH 17alpha-ethynylestradiol; 6-propyl-2-thiouracil; acrylamide.
Type: pseudo
RefSeq Status: PROVISIONAL
Previously known as: Tenascin X; tenascin XA; Tnxa
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Related Functional Gene: Tnxb  
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,031,091 - 4,032,446 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2204,026,471 - 4,027,826 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx204,726,417 - 4,727,772 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,088,169 - 4,089,524 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,625,339 - 4,626,694 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd204,424,655 - 4,426,010 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive205,512,505 - 5,513,860 (-)NCBILyon_Normotensive
Lyon_Hypertensive205,515,448 - 5,516,803 (-)NCBILyon_Hypertensive
F344_StmMcwi204,439,903 - 4,441,258 (-)NCBIF344_StmMcwi
Rnor_6.0204,485,316 - 4,486,671 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,564,672 - 6,566,027 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4204,128,066 - 4,129,421 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,002,274 - 4,003,629 (+)NCBICelera
RGSC_v3.1204,128,292 - 4,129,648 (-)NCBI
RH 3.4 Map2052.42RGD
Cytogenetic Map20p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Embryonic expression of tenascin-X suggests a role in limb, muscle, and heart development. Burch GH, etal., Dev Dyn 1995 Aug;203(4):491-504.
2. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
Additional References at PubMed
PMID:12477932   PMID:14604154   PMID:15646290   PMID:23533145   PMID:24370184   PMID:29101036   PMID:29915133  


Genomics

Comparative Map Data
Tnxa-ps1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8204,031,091 - 4,032,446 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2204,026,471 - 4,027,826 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx204,726,417 - 4,727,772 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0204,088,169 - 4,089,524 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,625,339 - 4,626,694 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd204,424,655 - 4,426,010 (-)NCBIDahl_SR_JrHsd
Lyon_Normotensive205,512,505 - 5,513,860 (-)NCBILyon_Normotensive
Lyon_Hypertensive205,515,448 - 5,516,803 (-)NCBILyon_Hypertensive
F344_StmMcwi204,439,903 - 4,441,258 (-)NCBIF344_StmMcwi
Rnor_6.0204,485,316 - 4,486,671 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0206,564,672 - 6,566,027 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4204,128,066 - 4,129,421 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera204,002,274 - 4,003,629 (+)NCBICelera
RGSC_v3.1204,128,292 - 4,129,648 (-)NCBI
RH 3.4 Map2052.42RGD
Cytogenetic Map20p12NCBI
TNXA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,008,420 - 32,013,023 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl632,008,614 - 32,012,472 (-)Ensemblhg38GRCh38
GRCh37631,976,197 - 31,980,800 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,084,369 - 32,088,120 (-)NCBIBuild 36Build 36hg18NCBI36
Celera633,575,958 - 33,580,680 (-)NCBICelera
Cytogenetic Map6p21.33NCBI
HuRef631,763,211 - 31,767,934 (-)NCBIHuRef
CHM1_1631,978,450 - 31,983,053 (-)NCBICHM1_1
T2T-CHM13v2.0631,861,626 - 31,866,229 (-)NCBIT2T-CHM13v2.0
Tnxa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,995,529 - 35,020,597 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,990,369 - 35,020,597 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381734,776,555 - 34,801,623 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,771,395 - 34,801,623 (+)Ensemblmm10GRCm38
MGSCv371734,913,500 - 34,938,568 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361734,913,504 - 34,914,870 (+)NCBIMGSCv36mm8
Celera1737,871,831 - 37,896,907 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.33NCBI

Variants

.
Variants in Tnxa-ps1
1 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362632310078622Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036263239244918Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH94616  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,026,509 - 4,026,599 (-)MAPPERmRatBN7.2
Rnor_6.0204,486,543 - 4,486,632NCBIRnor6.0
Rnor_5.0206,565,899 - 6,565,988UniSTSRnor5.0
RGSC_v3.4204,128,105 - 4,128,194UniSTSRGSC3.4
Celera204,003,501 - 4,003,590UniSTS
RH 3.4 Map2052.42UniSTS
Cytogenetic Map20p12UniSTS
RH134814  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2204,026,558 - 4,026,742 (-)MAPPERmRatBN7.2
Rnor_6.0204,486,400 - 4,486,583NCBIRnor6.0
Rnor_5.0206,565,756 - 6,565,939UniSTSRnor5.0
RGSC_v3.4204,128,154 - 4,128,337UniSTSRGSC3.4
Celera204,003,358 - 4,003,541UniSTS
Cytogenetic Map20p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 18 33 24 94 52 11 32 35 32 10 10

Sequence


RefSeq Acc Id: NR_024118
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8204,031,091 - 4,032,446 (-)NCBI
mRatBN7.2204,026,471 - 4,027,826 (-)NCBI
Dahl_SR_JrHsd204,424,655 - 4,426,010 (-)NCBI
Lyon_Normotensive205,512,505 - 5,513,860 (-)NCBI
Lyon_Hypertensive205,515,448 - 5,516,803 (-)NCBI
F344_StmMcwi204,439,903 - 4,441,258 (-)NCBI
Rnor_6.0204,485,316 - 4,486,671 (+)NCBI
Rnor_5.0206,564,672 - 6,566,027 (+)NCBI
RGSC_v3.4204,128,066 - 4,129,421 (-)RGD
Celera204,002,274 - 4,003,629 (+)RGD
Sequence:
Protein Sequences
GenBank Protein AAA91987 (Get FASTA)   NCBI Sequence Viewer  
  AAI68181 (Get FASTA)   NCBI Sequence Viewer  


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3887 AgrOrtholog
BioCyc Gene G2FUF-4594 BioCyc
NCBI Gene 25602 ENTREZGENE
PhenoGen Tnxa-ps1 PhenoGen
TIGR TC219362


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-06-09 Tnxa-ps1  tenascin XA, pseudogene 1  Tnxa  tenascin XA  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Tnxa  Tenascin X      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process plays a role in connective tissue cell migration and late muscle morphogenesis 634500