SHOX2 (short stature homeobox 2) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: SHOX2 (short stature homeobox 2) Sus scrofa
Analyze
Symbol: SHOX2
Name: short stature homeobox 2
RGD ID: 14020187
Description: ENCODES a protein that exhibits sequence-specific DNA binding (ortholog); INVOLVED IN cardiac atrium morphogenesis (ortholog); cardiac pacemaker cell differentiation (ortholog); cartilage development involved in endochondral bone morphogenesis (ortholog); ASSOCIATED WITH cleft palate (ortholog); lung cancer (ortholog); FOUND IN nucleus (inferred)
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: short stature homeobox protein 2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1397,879,281 - 97,890,447 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11397,879,586 - 97,892,276 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213106,074,270 - 106,084,447 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,IEA)

References
Additional References at PubMed
PMID:15679890  


Genomics

Comparative Map Data
SHOX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1397,879,281 - 97,890,447 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11397,879,586 - 97,892,276 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213106,074,270 - 106,084,447 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SHOX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3158,095,905 - 158,106,420 (-)EnsemblGRCh38hg38GRCh38
GRCh383158,095,905 - 158,106,420 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373157,813,694 - 157,824,209 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363159,296,494 - 159,306,630 (-)NCBINCBI36hg18NCBI36
Build 343159,297,570 - 159,306,541NCBI
Celera3156,237,551 - 156,247,714 (-)NCBI
Cytogenetic Map3q25.32NCBI
HuRef3155,210,551 - 155,220,711 (-)NCBIHuRef
CHM1_13157,777,104 - 157,787,273 (-)NCBICHM1_1
Shox2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39366,879,056 - 66,889,104 (-)NCBIGRCm39mm39
GRCm39 Ensembl366,879,060 - 66,889,104 (-)Ensembl
GRCm38366,971,723 - 66,981,771 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl366,971,727 - 66,981,771 (-)EnsemblGRCm38mm10GRCm38
MGSCv37366,777,188 - 66,785,693 (-)NCBIGRCm37mm9NCBIm37
MGSCv36367,061,195 - 67,069,700 (-)NCBImm8
Celera367,108,915 - 67,117,391 (-)NCBICelera
Cytogenetic Map3E1NCBI
cM Map330.76NCBI
Shox2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22151,217,049 - 151,227,180 (-)NCBI
Rnor_6.0 Ensembl2164,118,191 - 164,126,783 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02164,118,175 - 164,126,783 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02183,469,813 - 183,478,421 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42156,881,044 - 156,889,653 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12156,831,006 - 156,839,616 (-)NCBI
Celera2145,597,026 - 145,605,637 (-)NCBICelera
Cytogenetic Map2q31NCBI
Shox2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554488,937,610 - 8,947,890 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554488,937,656 - 8,947,890 (-)NCBIChiLan1.0ChiLan1.0
SHOX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13163,190,277 - 163,199,239 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3163,190,284 - 163,199,239 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03155,138,969 - 155,149,619 (-)NCBIMhudiblu_PPA_v0panPan3
SHOX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12351,484,696 - 51,492,586 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2351,484,421 - 51,492,566 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2351,357,238 - 51,365,278 (-)NCBI
ROS_Cfam_1.02352,123,573 - 52,131,639 (-)NCBI
UMICH_Zoey_3.12351,703,428 - 51,711,464 (-)NCBI
UNSW_CanFamBas_1.02351,755,484 - 51,763,458 (-)NCBI
UU_Cfam_GSD_1.02352,041,698 - 52,049,712 (-)NCBI
Shox2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560284,914,738 - 84,925,145 (+)NCBI
SpeTri2.0NW_0049365194,810,777 - 4,818,733 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHOX2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11532,684,598 - 32,694,640 (+)NCBI
ChlSab1.1 Ensembl1532,684,705 - 32,692,699 (+)Ensembl
Vero_WHO_p1.0NW_0236660415,251,405 - 5,261,933 (+)NCBI
Shox2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473035,826,631 - 35,836,141 (-)NCBI


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 hemolymphoid system musculoskeletal system nervous system reproductive system respiratory system
High
Medium 2
Low 2 4 2 2 1
Below cutoff 5 2 1 3 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000025053   ⟹   ENSSSCP00000020186
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1397,879,281 - 97,890,447 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000055948   ⟹   ENSSSCP00000050114
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1397,879,529 - 97,887,237 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000085360   ⟹   ENSSSCP00000061569
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1397,880,068 - 97,889,351 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000088555   ⟹   ENSSSCP00000074316
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1397,879,539 - 97,886,718 (-)Ensembl
RefSeq Acc Id: NM_001243352   ⟹   NP_001230281
RefSeq Status: VALIDATED
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11397,881,475 - 97,889,586 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005654033   ⟹   XP_005654090
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11397,879,586 - 97,892,276 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001230281 (Get FASTA)   NCBI Sequence Viewer  
  XP_005654090 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_005654090   ⟸   XM_005654033
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001230281   ⟸   NM_001243352
- UniProtKB: I3L828 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000074316   ⟸   ENSSSCT00000088555
RefSeq Acc Id: ENSSSCP00000020186   ⟸   ENSSSCT00000025053
RefSeq Acc Id: ENSSSCP00000050114   ⟸   ENSSSCT00000055948
RefSeq Acc Id: ENSSSCP00000061569   ⟸   ENSSSCT00000085360
Protein Domains
Homeobox   OAR


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000025238 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00070001191 UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000020186 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00000050114 UniProtKB/TrEMBL
  ENSSSCP00000061569 UniProtKB/TrEMBL
  ENSSSCP00000074316 UniProtKB/TrEMBL
  ENSSSCP00070001941 UniProtKB/TrEMBL
  ENSSSCP00070001960 UniProtKB/TrEMBL
  ENSSSCP00070001969 UniProtKB/TrEMBL
  ENSSSCP00070001981 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000025053 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000055948 UniProtKB/TrEMBL
  ENSSSCT00000085360 UniProtKB/TrEMBL
  ENSSSCT00000088555 UniProtKB/TrEMBL
  ENSSSCT00070002322 UniProtKB/TrEMBL
  ENSSSCT00070002341 UniProtKB/TrEMBL
  ENSSSCT00070002354 UniProtKB/TrEMBL
  ENSSSCT00070002370 UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  HTH_motif UniProtKB/TrEMBL
  OAR_dom UniProtKB/TrEMBL
KEGG Report ssc:100628206 UniProtKB/TrEMBL
NCBI Gene SHOX2 ENTREZGENE
Pfam Homeodomain UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
PRINTS HTHREPRESSR UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
  OAR UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A287B137_PIG UniProtKB/TrEMBL
  A0A4X1SHY9_PIG UniProtKB/TrEMBL
  A0A4X1SI36_PIG UniProtKB/TrEMBL
  A0A4X1SI45_PIG UniProtKB/TrEMBL
  A0A4X1SI66_PIG UniProtKB/TrEMBL
  A0A5G2QBY7_PIG UniProtKB/TrEMBL
  A0A5G2RCZ0_PIG UniProtKB/TrEMBL
  I3L828 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:107170 ENTREZGENE