Tnxb (tenascin XB) - Rat Genome Database

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Gene: Tnxb (tenascin XB) Rattus norvegicus
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Symbol: Tnxb
Name: tenascin XB
RGD ID: 1594402
Description: Predicted to enable collagen binding activity; collagen fibril binding activity; and heparin binding activity. Predicted to be involved in collagen metabolic process; elastic fiber assembly; and positive regulation of collagen fibril organization. Predicted to act upstream of or within several processes, including collagen fibril organization; regulation of JUN kinase activity; and triglyceride metabolic process. Predicted to be located in extracellular matrix; extracellular space; and intracellular membrane-bounded organelle. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome and vesicoureteral reflux. Orthologous to human TNXB (tenascin XB); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: MGC188001; tenascin X pseudogene; Tnx
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: Tnxa-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
RGSC_v3.4204,133,875 - 4,178,049 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1204,133,161 - 4,134,180 (-)NCBI
Celera203,953,496 - 3,997,652 (+)NCBICelera
Cytogenetic Map20p12NCBI


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-tribromophenol  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-palmitoylglycerol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP,ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
ammonium chloride  (EXP)
antimycin A  (ISO)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
cannabidiol  (ISO)
cantharidin  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
CGP 52608  (ISO)
chrysene  (ISO)
clothianidin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (ISO)
dexamethasone  (ISO)
diiodine  (ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
fulvestrant  (ISO)
glyphosate  (ISO)
herbicide  (ISO)
indometacin  (ISO)
isotretinoin  (ISO)
menadione  (ISO)
methotrexate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
paracetamol  (ISO)
paricalcitol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phosphorus atom  (ISO)
phosphorus(.)  (ISO)
Ptaquiloside  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
silicon dioxide  (EXP,ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sotorasib  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
toluene  (ISO)
trametinib  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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
4. A recessive form of the Ehlers-Danlos syndrome caused by tenascin-X deficiency. Schalkwijk J, etal., N Engl J Med. 2001 Oct 18;345(16):1167-75.
Additional References at PubMed
PMID:7512972   PMID:7528728   PMID:8856503   PMID:11925569   PMID:12410392   PMID:12419962   PMID:12477932   PMID:15102077   PMID:15194424   PMID:15212943   PMID:15242785   PMID:15298681  
PMID:15340236   PMID:16278880   PMID:16551009   PMID:20551380   PMID:23376485   PMID:23533145   PMID:24563484   PMID:27068509   PMID:27559042  


Genomics

Comparative Map Data
Tnxb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
RGSC_v3.4204,133,875 - 4,178,049 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1204,133,161 - 4,134,180 (-)NCBI
Celera203,953,496 - 3,997,652 (+)NCBICelera
Cytogenetic Map20p12NCBI
TNXB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38632,041,153 - 32,109,338 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl632,041,153 - 32,115,334 (-)EnsemblGRCh38hg38GRCh38
GRCh37632,008,930 - 32,077,115 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36632,116,911 - 32,185,131 (-)NCBINCBI36Build 36hg18NCBI36
Build 34632,116,910 - 32,121,883NCBI
Celera633,575,958 - 33,644,194 (-)NCBICelera
Cytogenetic Map6p21.33-p21.32NCBI
HuRef631,763,211 - 31,831,274 (-)NCBIHuRef
CHM1_1632,011,143 - 32,079,361 (-)NCBICHM1_1
T2T-CHM13v2.0631,894,357 - 31,962,530 (-)NCBIT2T-CHM13v2.0
Tnxb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391734,879,427 - 34,938,789 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1734,879,431 - 34,938,789 (+)EnsemblGRCm39 Ensembl
GRCm381734,660,453 - 34,719,815 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1734,660,457 - 34,719,815 (+)EnsemblGRCm38mm10GRCm38
MGSCv371734,807,480 - 34,856,572 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,278,591 - 34,327,683 (+)NCBIMGSCv36mm8
Celera1737,765,706 - 37,815,870 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.24NCBI
Tnxb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955437511,963 - 553,856 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955437516,713 - 561,188 (-)NCBIChiLan1.0ChiLan1.0
LOC100992963
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2546,503,672 - 46,571,952 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1642,465,152 - 42,532,960 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,687,994 - 31,756,279 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,572,833 - 32,637,194 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,571,199 - 32,626,155 (-)Ensemblpanpan1.1panPan2
TNXB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,453,227 - 1,510,171 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,453,260 - 1,509,749 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,587,966 - 1,644,804 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,595,038 - 1,648,746 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1121,452,523 - 1,512,316 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,520,713 - 1,577,568 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,587,312 - 1,644,152 (-)NCBIUU_Cfam_GSD_1.0
Tnxb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494636,010,582 - 36,068,641 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,500,200 - 1,550,564 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,492,725 - 1,550,762 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TNXB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl724,088,873 - 24,150,596 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1724,088,873 - 24,155,815 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,681,443 - 27,723,267 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TNXB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11739,919,839 - 39,988,087 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1739,919,772 - 39,986,868 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604431,960,490 - 32,011,834 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tnxb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475424,198,979 - 24,253,185 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:110
Count of miRNA genes:95
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000048985
Prediction methods:Microtar, Miranda, Rnahybrid
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.


Expression

RNA-SEQ Expression


Sequence


Protein Sequences
Protein RefSeqs NP_001403300 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD17201 (Get FASTA)   NCBI Sequence Viewer  
  AAI66501 (Get FASTA)   NCBI Sequence Viewer  
  AAI68189 (Get FASTA)   NCBI Sequence Viewer  
Protein Domains
Fibrinogen C-terminal   Fibronectin type-III


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594402 AgrOrtholog
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
  3.90.215.10 UniProtKB/TrEMBL
InterPro ECM_Regulatory_Proteins UniProtKB/TrEMBL
  Fibrinogen-like_C UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_1 UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_dom UniProtKB/TrEMBL
  Fibrinogen_CS UniProtKB/TrEMBL
  FN3_dom UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
NCBI Gene 415089 ENTREZGENE
PANTHER PTHR46708:SF3 UniProtKB/TrEMBL
  TENASCIN UniProtKB/TrEMBL
Pfam Fibrinogen_C UniProtKB/TrEMBL
  fn3 UniProtKB/TrEMBL
PhenoGen Tnxb PhenoGen
PROSITE FIBRINOGEN_C_1 UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
SMART FBG UniProtKB/TrEMBL
  FN3 UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/TrEMBL
  SSF56496 UniProtKB/TrEMBL
UniProt B2GV27_RAT UniProtKB/TrEMBL
  B4F793_RAT UniProtKB/TrEMBL
  B4F7A0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-03 Tnxb  tenascin XB  Tnxb  tenascin XB  Data merged from RGD:621041 737654 APPROVED
2008-09-03 Tnxb  tenascin XB  Tnx  tenascin X pseudogene  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-11-20 Tnx  tenascin X pseudogene      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-07-08 Tnxb  tenascin XB      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Tnxb  tenascin XB      Symbol and Name status set to provisional 70820 PROVISIONAL