Tsx (testis specific X-linked gene) - Rat Genome Database

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Gene: Tsx (testis specific X-linked gene) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Tsx
Name: testis specific X-linked gene
RGD ID: 3914
Description: Predicted to be located in membrane.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: testis specific X-linked; testis-specific protein TSX
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X72,493,147 - 72,503,653 (+)NCBIGRCr8
mRatBN7.2X68,426,668 - 68,437,887 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX68,361,969 - 68,437,887 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX69,936,574 - 69,947,080 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X73,436,811 - 73,447,317 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X70,997,997 - 71,008,503 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X74,269,513 - 74,283,819 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX74,273,182 - 74,283,819 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X75,075,366 - 75,089,673 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X91,398,417 - 91,408,922 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X91,471,849 - 91,482,355 (+)NCBI
CeleraX69,795,006 - 69,805,512 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. A 94 kb genomic sequence 3' to the murine Xist gene reveals an AT rich region containing a new testis specific gene Tsx. Simmler MC, etal., Hum Mol Genet 1996 Nov;5(11):1713-26.
4. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data

Genomics

Variants

.
Variants in Tsx
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:40
Count of miRNA genes:34
Interacting mature miRNAs:38
Transcripts:ENSRNOT00000003922
Prediction methods:Miranda, Pita, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
RH139668  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X68,437,566 - 68,437,761 (+)MAPPERmRatBN7.2
Rnor_6.0X74,283,499 - 74,283,693NCBIRnor6.0
Rnor_5.0X75,089,353 - 75,089,547UniSTSRnor5.0
RGSC_v3.4X91,408,602 - 91,408,796UniSTSRGSC3.4
CeleraX69,805,192 - 69,805,386UniSTS
Cytogenetic MapXq31UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 1
Medium 14 14 14 7 18
Low 3 3 35 20 14 20 3 3 57 28 22 10 3
Below cutoff 36 7 6 5 6 3 5 17 1 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003922   ⟹   ENSRNOP00000003922
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,423,719 - 68,437,887 (+)Ensembl
Rnor_6.0 EnsemblX74,273,182 - 74,283,819 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076956   ⟹   ENSRNOP00000068153
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,362,027 - 68,437,704 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077003   ⟹   ENSRNOP00000067927
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,361,969 - 68,437,887 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000098584   ⟹   ENSRNOP00000093183
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,427,451 - 68,435,419 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101872   ⟹   ENSRNOP00000078564
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX68,361,969 - 68,402,819 (+)Ensembl
RefSeq Acc Id: NM_019203   ⟹   NP_062076
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X72,493,147 - 72,503,653 (+)NCBI
mRatBN7.2X68,427,381 - 68,437,887 (+)NCBI
Rnor_6.0X74,273,182 - 74,283,819 (+)NCBI
Rnor_5.0X75,075,366 - 75,089,673 (+)NCBI
RGSC_v3.4X91,398,417 - 91,408,922 (+)RGD
CeleraX69,795,006 - 69,805,512 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_062076 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA68130 (Get FASTA)   NCBI Sequence Viewer  
  EDM07189 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003922
  ENSRNOP00000003922.4
  ENSRNOP00000067927.2
  ENSRNOP00000068153.2
  ENSRNOP00000093183.1
GenBank Protein P70537 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_062076   ⟸   NM_019203
- UniProtKB: P70537 (UniProtKB/Swiss-Prot),   A6IUZ1 (UniProtKB/TrEMBL),   A0A8L2Q150 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003922   ⟸   ENSRNOT00000003922
RefSeq Acc Id: ENSRNOP00000068153   ⟸   ENSRNOT00000076956
RefSeq Acc Id: ENSRNOP00000067927   ⟸   ENSRNOT00000077003
RefSeq Acc Id: ENSRNOP00000078564   ⟸   ENSRNOT00000101872
RefSeq Acc Id: ENSRNOP00000093183   ⟸   ENSRNOT00000098584
Protein Domains
Golgin subfamily A member 7/ERF4

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P70537-F1-model_v2 AlphaFold P70537 1-144 view protein structure

Transcriptome

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

Promoters
RGD ID:13701890
Promoter ID:EPDNEW_R12414
Type:multiple initiation site
Name:Tsx_1
Description:testis specific X-linked gene
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X74,273,176 - 74,273,236EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3914 AgrOrtholog
BioCyc Gene G2FUF-2028 BioCyc
Ensembl Genes ENSRNOG00000002925 Ensembl
  ENSRNOG00000037919 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003922 ENTREZGENE
  ENSRNOT00000003922.5 UniProtKB/TrEMBL
  ENSRNOT00000076956.3 UniProtKB/TrEMBL
  ENSRNOT00000077003.2 UniProtKB/TrEMBL
  ENSRNOT00000098584.1 UniProtKB/TrEMBL
InterPro CHIC1/2 UniProtKB/TrEMBL
  Golgin_A_7/ERF4 UniProtKB/TrEMBL
  TSX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29391 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 29391 ENTREZGENE
PANTHER CYSTEINE-RICH HYDROPHOBIC DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR13005 UniProtKB/TrEMBL
Pfam DUF5404 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Erf4 UniProtKB/TrEMBL
PhenoGen Tsx PhenoGen
RatGTEx ENSRNOG00000002925 RatGTEx
  ENSRNOG00000037919 RatGTEx
TIGR TC234238
UniProt A0A096MIY9_RAT UniProtKB/TrEMBL
  A0A096MJJ5_RAT UniProtKB/TrEMBL
  A0A8I6AJI0_RAT UniProtKB/TrEMBL
  A0A8L2Q150 ENTREZGENE, UniProtKB/TrEMBL
  A6IUZ1 ENTREZGENE, UniProtKB/TrEMBL
  P70537 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Tsx  testis specific X-linked gene      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_transcript gene is part of the X inactivation centre 70043