SHOX2 (SHOX homeobox 2) - Rat Genome Database

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Pathways
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Gene: SHOX2 (SHOX homeobox 2) Homo sapiens
Analyze
Symbol: SHOX2
Name: SHOX homeobox 2 (Ensembl:short stature homeobox 2)
RGD ID: 736918
HGNC Page HGNC:10854
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in heart development and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including heart development; positive regulation of cell population proliferation; and skeletal system development. Predicted to be part of chromatin. Predicted to be active in nucleus. Implicated in lung cancer.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: homeobox protein Og12X; OG12; OG12X; paired-related homeobox protein SHOT; short stature homeobox 2; short stature homeobox protein 2; SHOT; SHOX homologous gene on chromosome 3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383158,095,905 - 158,106,420 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3158,095,905 - 158,106,420 (-)EnsemblGRCh38hg38GRCh38
GRCh373157,813,694 - 157,824,209 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363159,296,494 - 159,306,630 (-)NCBINCBI36Build 36hg18NCBI36
Build 343159,297,570 - 159,306,541NCBI
Celera3156,237,551 - 156,247,714 (-)NCBICelera
Cytogenetic Map3q25.32NCBI
HuRef3155,210,551 - 155,220,711 (-)NCBIHuRef
CHM1_13157,777,104 - 157,787,273 (-)NCBICHM1_1
T2T-CHM13v2.03160,870,630 - 160,881,158 (-)NCBIT2T-CHM13v2.0
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

Biological Process
cardiac atrium morphogenesis  (IEA,ISO)
cardiac pacemaker cell differentiation  (IEA,ISS)
cardiac right atrium morphogenesis  (IEA,ISS)
cartilage development involved in endochondral bone morphogenesis  (IEA,ISO)
chondrocyte development  (IEA,ISO)
chondrocyte differentiation  (IEA,ISO)
embryonic digestive tract morphogenesis  (IEA,ISO)
embryonic forelimb morphogenesis  (IEA,ISO)
embryonic limb morphogenesis  (IEA,ISO)
embryonic morphogenesis  (IEA,ISO)
embryonic skeletal joint morphogenesis  (IEA,ISO)
heart valve development  (IEA,ISO)
mesenchymal cell proliferation  (IEA,ISO)
muscle tissue morphogenesis  (IEA)
negative regulation of transcription by RNA polymerase II  (IEA,ISS)
nervous system development  (TAS)
osteoblast differentiation  (IEA,ISO)
positive regulation of axonogenesis  (IEA)
positive regulation of mesenchymal cell proliferation  (IEA,ISO)
positive regulation of skeletal muscle fiber development  (IEA)
positive regulation of smoothened signaling pathway  (IEA,ISO)
positive regulation of stem cell proliferation  (IEA,ISO)
regulation of branching morphogenesis of a nerve  (IEA)
regulation of chondrocyte differentiation  (IEA,ISO)
regulation of DNA-templated transcription  (IEA)
regulation of heart rate  (IEA,ISS)
regulation of transcription by RNA polymerase II  (IBA,IEA)
sinoatrial node cell development  (IEA,ISS)
sinoatrial node development  (IEA,ISS)
sinoatrial valve development  (IEA,ISS)
skeletal system development  (TAS)
smoothened signaling pathway  (IEA,ISO)
stem cell proliferation  (IEA,ISO)

Cellular Component
chromatin  (ISA)
nucleus  (IBA,IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Analysis of SHOX2 methylation as an aid to cytology in lung cancer diagnosis. Ilse P, etal., Cancer Genomics Proteomics. 2014 Sep-Oct;11(5):251-8.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Shox2-deficient mice exhibit a rare type of incomplete clefting of the secondary palate. Yu L, etal., Development. 2005 Oct;132(19):4397-406. Epub 2005 Sep 1.
Additional References at PubMed
PMID:9466998   PMID:9482898   PMID:9858825   PMID:12477932   PMID:14702039   PMID:14759258   PMID:15489334   PMID:16344560   PMID:19274049   PMID:19322201   PMID:19336002   PMID:19453261  
PMID:20211142   PMID:20858598   PMID:21047392   PMID:21426551   PMID:21694641   PMID:21873635   PMID:22094256   PMID:22108652   PMID:22555092   PMID:23038774   PMID:23563607   PMID:23851611  
PMID:24026539   PMID:24136974   PMID:24161943   PMID:24386354   PMID:24421874   PMID:24705354   PMID:24746361   PMID:25429064   PMID:25533636   PMID:25675432   PMID:26697824   PMID:27036009  
PMID:27138930   PMID:27544059   PMID:27660666   PMID:27840009   PMID:27999621   PMID:28069583   PMID:28325362   PMID:29610456   PMID:30021884   PMID:30443179   PMID:31167696   PMID:31183590  
PMID:32266538   PMID:32683847   PMID:33167712   PMID:34275516   PMID:34308848   PMID:34465361   PMID:35088378   PMID:37499664  


Genomics

Comparative Map Data
SHOX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383158,095,905 - 158,106,420 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3158,095,905 - 158,106,420 (-)EnsemblGRCh38hg38GRCh38
GRCh373157,813,694 - 157,824,209 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363159,296,494 - 159,306,630 (-)NCBINCBI36Build 36hg18NCBI36
Build 343159,297,570 - 159,306,541NCBI
Celera3156,237,551 - 156,247,714 (-)NCBICelera
Cytogenetic Map3q25.32NCBI
HuRef3155,210,551 - 155,220,711 (-)NCBIHuRef
CHM1_13157,777,104 - 157,787,273 (-)NCBICHM1_1
T2T-CHM13v2.03160,870,630 - 160,881,158 (-)NCBIT2T-CHM13v2.0
Shox2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39366,879,056 - 66,889,104 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl366,879,060 - 66,889,104 (-)EnsemblGRCm39 Ensembl
GRCm38366,971,723 - 66,981,771 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl366,971,727 - 66,981,771 (-)EnsemblGRCm38mm10GRCm38
MGSCv37366,777,188 - 66,785,693 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36367,061,195 - 67,069,700 (-)NCBIMGSCv36mm8
Celera367,108,915 - 67,117,391 (-)NCBICelera
Cytogenetic Map3E1NCBI
cM Map330.76NCBI
Shox2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82153,524,324 - 153,537,571 (-)NCBIGRCr8
mRatBN7.22151,217,049 - 151,227,180 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2151,217,552 - 151,227,143 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2158,353,974 - 158,363,583 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02156,404,472 - 156,414,073 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02151,037,220 - 151,046,824 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02164,118,175 - 164,126,783 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2164,118,191 - 164,126,783 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02183,469,813 - 183,478,421 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42156,881,044 - 156,889,653 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v22156,001,278 - 156,011,606 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13156,005,878 - 156,016,648 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03155,138,969 - 155,149,619 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13163,190,277 - 163,199,239 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3163,190,284 - 163,199,239 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02352,123,573 - 52,131,639 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2352,123,242 - 52,131,401 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12351,703,428 - 51,711,464 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02351,755,484 - 51,763,458 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02352,041,698 - 52,049,712 (-)NCBIUU_Cfam_GSD_1.0
Shox2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560284,914,738 - 84,925,145 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365194,809,687 - 4,818,792 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365194,810,777 - 4,818,733 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHOX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1397,879,281 - 97,889,785 (-)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
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11532,684,598 - 32,694,640 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1532,684,705 - 32,692,699 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660415,251,405 - 5,261,933 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shox2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473035,825,922 - 35,835,756 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473035,826,631 - 35,836,141 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SHOX2
29 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q24-26.32(chr3:147442566-178522531)x3 copy number gain See cases [RCV000051724] Chr3:147442566..178522531 [GRCh38]
Chr3:147160353..178240319 [GRCh37]
Chr3:148643043..179723013 [NCBI36]
Chr3:3q24-26.32		 pathogenic
GRCh38/hg38 3q24-29(chr3:147521892-198096565)x3 copy number gain See cases [RCV000051725] Chr3:147521892..198096565 [GRCh38]
Chr3:147239679..197823436 [GRCh37]
Chr3:148722369..199307833 [NCBI36]
Chr3:3q24-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:157293378-198134727)x3 copy number gain See cases [RCV000051726] Chr3:157293378..198134727 [GRCh38]
Chr3:157011167..197861598 [GRCh37]
Chr3:158493861..199345995 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q22.3-29(chr3:137126982-198110178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|See cases [RCV000051723] Chr3:137126982..198110178 [GRCh38]
Chr3:136845824..197837049 [GRCh37]
Chr3:138328514..199321446 [NCBI36]
Chr3:3q22.3-29		 pathogenic
NM_001163678.2(SHOX2):c.224_232dup (p.Gly75_Gly77dup) duplication not specified [RCV000173295] Chr3:158105792..158105793 [GRCh38]
Chr3:157823581..157823582 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.222C>T (p.Gly74=) single nucleotide variant not provided [RCV000173294] Chr3:158105803 [GRCh38]
Chr3:157823592 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q25.1-29(chr3:152100512-198118383)x3 copy number gain See cases [RCV000139435] Chr3:152100512..198118383 [GRCh38]
Chr3:151818301..197845254 [GRCh37]
Chr3:153300991..199329651 [NCBI36]
Chr3:3q25.1-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156321878-198113452)x3 copy number gain See cases [RCV000140849] Chr3:156321878..198113452 [GRCh38]
Chr3:156039667..197840323 [GRCh37]
Chr3:157522361..199324720 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156118441-198125115)x3 copy number gain See cases [RCV000142310] Chr3:156118441..198125115 [GRCh38]
Chr3:155836230..197851986 [GRCh37]
Chr3:157318924..199336383 [NCBI36]
Chr3:3q25.31-29		 pathogenic
NM_001163678.2(SHOX2):c.346+590G>A single nucleotide variant not provided [RCV000175747] Chr3:158105089 [GRCh38]
Chr3:157822878 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3q24-29(chr3:142995020-192997215)x4 copy number gain See cases [RCV000240256] Chr3:142995020..192997215 [GRCh37]
Chr3:3q24-29		 pathogenic
NM_001163678.2(SHOX2):c.295A>T (p.Met99Leu) single nucleotide variant not provided [RCV000388360] Chr3:158105730 [GRCh38]
Chr3:157823519 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3q25.32-26.33(chr3:157128738-181637333)x3 copy number gain See cases [RCV000446611] Chr3:157128738..181637333 [GRCh37]
Chr3:3q25.32-26.33		 pathogenic
GRCh37/hg19 3q25.2-29(chr3:152356847-197851986)x3 copy number gain See cases [RCV000448608] Chr3:152356847..197851986 [GRCh37]
Chr3:3q25.2-29		 pathogenic
GRCh37/hg19 3q24-26.2(chr3:147180945-168415875)x1 copy number loss See cases [RCV000448130] Chr3:147180945..168415875 [GRCh37]
Chr3:3q24-26.2		 pathogenic
NM_001163678.2(SHOX2):c.128G>A (p.Cys43Tyr) single nucleotide variant Inborn genetic diseases [RCV003255814] Chr3:158105897 [GRCh38]
Chr3:157823686 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.766C>G (p.Leu256Val) single nucleotide variant Inborn genetic diseases [RCV003271651] Chr3:158098221 [GRCh38]
Chr3:157816010 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.169C>G (p.Arg57Gly) single nucleotide variant Inborn genetic diseases [RCV003287882] Chr3:158105856 [GRCh38]
Chr3:157823645 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
NM_001163678.2(SHOX2):c.556G>A (p.Val186Ile) single nucleotide variant Inborn genetic diseases [RCV003270425] Chr3:158100311 [GRCh38]
Chr3:157818100 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
NM_001163678.2(SHOX2):c.630C>T (p.Ala210=) single nucleotide variant not provided [RCV000961131] Chr3:158099932 [GRCh38]
Chr3:157817721 [GRCh37]
Chr3:3q25.32		 benign
GRCh37/hg19 3q25.32(chr3:157620773-158351532)x1 copy number loss not provided [RCV000847772] Chr3:157620773..158351532 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3q25.32(chr3:157542717-158388665)x3 copy number gain not provided [RCV000847182] Chr3:157542717..158388665 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.304G>A (p.Ala102Thr) single nucleotide variant not provided [RCV001092436] Chr3:158105721 [GRCh38]
Chr3:157823510 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3q25.31-25.33(chr3:156812581-160154747)x3 copy number gain See cases [RCV001194528] Chr3:156812581..160154747 [GRCh37]
Chr3:3q25.31-25.33		 uncertain significance
GRCh37/hg19 3q22.3-26.1(chr3:138145289-162275610)x3 copy number gain See cases [RCV001194586] Chr3:138145289..162275610 [GRCh37]
Chr3:3q22.3-26.1		 pathogenic
GRCh37/hg19 3q25.32(chr3:157666169-158146714)x3 copy number gain not provided [RCV001259719] Chr3:157666169..158146714 [GRCh37]
Chr3:3q25.32		 uncertain significance
GRCh37/hg19 3q22.3-26.1(chr3:138173683-162494699) copy number gain Global developmental delay [RCV001352648] Chr3:138173683..162494699 [GRCh37]
Chr3:3q22.3-26.1		 pathogenic
GRCh37/hg19 3q23-25.32(chr3:142729607-157921084)x3 copy number gain Brachycephaly [RCV001801182] Chr3:142729607..157921084 [GRCh37]
Chr3:3q23-25.32		 pathogenic
GRCh37/hg19 3q24-26.1(chr3:143439359-165252122)x1 copy number loss not provided [RCV001795847] Chr3:143439359..165252122 [GRCh37]
Chr3:3q24-26.1		 pathogenic
GRCh37/hg19 3q25.31-25.33(chr3:156768935-160158553) copy number gain not specified [RCV002053381] Chr3:156768935..160158553 [GRCh37]
Chr3:3q25.31-25.33		 uncertain significance
GRCh37/hg19 3q25.32-26.33(chr3:157128738-181637333) copy number gain not specified [RCV002053382] Chr3:157128738..181637333 [GRCh37]
Chr3:3q25.32-26.33		 pathogenic
GRCh37/hg19 3q24-25.33(chr3:145486960-160504834) copy number gain not specified [RCV002053375] Chr3:145486960..160504834 [GRCh37]
Chr3:3q24-25.33		 pathogenic
NM_001163678.2(SHOX2):c.136G>C (p.Ala46Pro) single nucleotide variant Inborn genetic diseases [RCV003255816] Chr3:158105889 [GRCh38]
Chr3:157823678 [GRCh37]
Chr3:3q25.32		 likely benign
GRCh37/hg19 3q13.31-26.31(chr3:116620308-172042292)x3 copy number gain not provided [RCV002472621] Chr3:116620308..172042292 [GRCh37]
Chr3:3q13.31-26.31		 pathogenic
NM_001163678.2(SHOX2):c.14C>A (p.Thr5Lys) single nucleotide variant Inborn genetic diseases [RCV002732710] Chr3:158106011 [GRCh38]
Chr3:157823800 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.776A>G (p.His259Arg) single nucleotide variant Inborn genetic diseases [RCV002882689] Chr3:158098211 [GRCh38]
Chr3:157816000 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.757C>T (p.His253Tyr) single nucleotide variant Inborn genetic diseases [RCV002823019] Chr3:158098230 [GRCh38]
Chr3:157816019 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.245G>A (p.Gly82Glu) single nucleotide variant Inborn genetic diseases [RCV002826770] Chr3:158105780 [GRCh38]
Chr3:157823569 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.346+610T>G single nucleotide variant Inborn genetic diseases [RCV002764871] Chr3:158105069 [GRCh38]
Chr3:157822858 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.256G>A (p.Gly86Arg) single nucleotide variant Inborn genetic diseases [RCV002674727] Chr3:158105769 [GRCh38]
Chr3:157823558 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.622A>C (p.Ile208Leu) single nucleotide variant Inborn genetic diseases [RCV002941364] Chr3:158099940 [GRCh38]
Chr3:157817729 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.343G>A (p.Glu115Lys) single nucleotide variant Inborn genetic diseases [RCV002657021] Chr3:158105682 [GRCh38]
Chr3:157823471 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.278C>T (p.Pro93Leu) single nucleotide variant Inborn genetic diseases [RCV002678792] Chr3:158105747 [GRCh38]
Chr3:157823536 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.130A>G (p.Thr44Ala) single nucleotide variant Inborn genetic diseases [RCV003255815] Chr3:158105895 [GRCh38]
Chr3:157823684 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.839A>G (p.Asp280Gly) single nucleotide variant Inborn genetic diseases [RCV003281266] Chr3:158098148 [GRCh38]
Chr3:157815937 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.311G>C (p.Arg104Thr) single nucleotide variant Inborn genetic diseases [RCV003175233] Chr3:158105714 [GRCh38]
Chr3:157823503 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.857C>G (p.Ser286Trp) single nucleotide variant Inborn genetic diseases [RCV003202209] Chr3:158098130 [GRCh38]
Chr3:157815919 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.115G>C (p.Glu39Gln) single nucleotide variant Inborn genetic diseases [RCV003371224] Chr3:158105910 [GRCh38]
Chr3:157823699 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.760C>A (p.Pro254Thr) single nucleotide variant Inborn genetic diseases [RCV003354835] Chr3:158098227 [GRCh38]
Chr3:157816016 [GRCh37]
Chr3:3q25.32		 uncertain significance
NM_001163678.2(SHOX2):c.355G>A (p.Glu119Lys) single nucleotide variant Inborn genetic diseases [RCV003369983] Chr3:158102878 [GRCh38]
Chr3:157820667 [GRCh37]
Chr3:3q25.32		 uncertain significance
Single allele duplication not provided [RCV003448680] Chr3:140154329..197847235 [GRCh37]
Chr3:3q23-29		 pathogenic
NM_001163678.2(SHOX2):c.852C>G (p.Ala284=) single nucleotide variant not provided [RCV003434783] Chr3:158098135 [GRCh38]
Chr3:157815924 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.537G>T (p.Leu179=) single nucleotide variant SHOX2-related condition [RCV003977078] Chr3:158102696 [GRCh38]
Chr3:157820485 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.63G>A (p.Glu21=) single nucleotide variant SHOX2-related condition [RCV003961400] Chr3:158105962 [GRCh38]
Chr3:157823751 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.174G>A (p.Ala58=) single nucleotide variant SHOX2-related condition [RCV003949859] Chr3:158105851 [GRCh38]
Chr3:157823640 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.556-6C>G single nucleotide variant SHOX2-related condition [RCV003934412] Chr3:158100317 [GRCh38]
Chr3:157818106 [GRCh37]
Chr3:3q25.32		 likely benign
NM_001163678.2(SHOX2):c.306C>G (p.Ala102=) single nucleotide variant SHOX2-related condition [RCV003943929] Chr3:158105719 [GRCh38]
Chr3:157823508 [GRCh37]
Chr3:3q25.32		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1664
Count of miRNA genes:612
Interacting mature miRNAs:701
Transcripts:ENST00000389589, ENST00000425436, ENST00000441443, ENST00000483851, ENST00000490689, ENST00000554685
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.

Markers in Region
RH92222  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh373157,813,881 - 157,814,030UniSTSGRCh37
Build 363159,296,575 - 159,296,724RGDNCBI36
Celera3156,237,632 - 156,237,781RGD
Cytogenetic Map3q25.32UniSTS
HuRef3155,210,632 - 155,210,781UniSTS
GeneMap99-GB4 RH Map3582.79UniSTS
SGC44267  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map3q25.32UniSTS
GeneMap99-GB4 RH Map3582.79UniSTS
Whitehead-RH Map3715.1UniSTS
NCBI RH Map31371.5UniSTS


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 23 698 12 6 67 2 1887 38 690 12 59 75 5 526 1301
Low 779 1191 723 187 535 33 2199 1491 315 62 815 886 164 342 1406 1
Below cutoff 1528 970 763 237 1113 237 225 663 2087 170 517 605 1 328 81 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_047079 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001163678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_003030 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_006884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006713727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006713728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017007053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017007054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017007055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047448731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054347563 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054347564 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054347565 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054347566 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA450208 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC112502 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF022654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ002368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK095338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC008829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX331739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA447204 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000389589   ⟹   ENSP00000374240
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3158,097,159 - 158,106,160 (-)Ensembl
RefSeq Acc Id: ENST00000425436   ⟹   ENSP00000398704
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3158,097,080 - 158,102,887 (-)Ensembl
RefSeq Acc Id: ENST00000441443   ⟹   ENSP00000397099
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3158,096,011 - 158,106,050 (-)Ensembl
RefSeq Acc Id: ENST00000483851   ⟹   ENSP00000419362
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3158,095,905 - 158,106,420 (-)Ensembl
RefSeq Acc Id: ENST00000490689
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3158,095,954 - 158,105,294 (-)Ensembl
RefSeq Acc Id: ENST00000554685   ⟹   ENSP00000479329
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3158,099,885 - 158,105,718 (-)Ensembl
RefSeq Acc Id: NM_001163678   ⟹   NP_001157150
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,095,905 - 158,106,420 (-)NCBI
GRCh373157,813,800 - 157,823,952 (-)RGD
Celera3156,237,551 - 156,247,714 (-)RGD
HuRef3155,210,551 - 155,220,711 (-)ENTREZGENE
CHM1_13157,777,104 - 157,787,273 (-)NCBI
T2T-CHM13v2.03160,870,630 - 160,881,158 (-)NCBI
Sequence:
RefSeq Acc Id: NM_003030   ⟹   NP_003021
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,096,011 - 158,106,163 (-)NCBI
GRCh373157,813,800 - 157,823,952 (-)RGD
Build 363159,296,494 - 159,303,520 (-)NCBI Archive
Celera3156,237,551 - 156,247,714 (-)RGD
HuRef3155,210,551 - 155,220,711 (-)ENTREZGENE
CHM1_13157,777,104 - 157,787,273 (-)NCBI
T2T-CHM13v2.03160,870,736 - 160,880,901 (-)NCBI
Sequence:
RefSeq Acc Id: NM_006884   ⟹   NP_006875
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,096,011 - 158,106,163 (-)NCBI
GRCh373157,813,800 - 157,823,952 (-)RGD
Build 363159,296,494 - 159,306,630 (-)NCBI Archive
Celera3156,237,551 - 156,247,714 (-)RGD
HuRef3155,210,551 - 155,220,711 (-)ENTREZGENE
CHM1_13157,777,104 - 157,787,273 (-)NCBI
T2T-CHM13v2.03160,870,736 - 160,880,901 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006713727   ⟹   XP_006713790
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,095,905 - 158,106,420 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006713728   ⟹   XP_006713791
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,095,905 - 158,105,441 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017007053   ⟹   XP_016862542
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,095,905 - 158,105,441 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047448731   ⟹   XP_047304687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,095,905 - 158,105,005 (-)NCBI
RefSeq Acc Id: XM_054347563   ⟹   XP_054203538
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.03160,870,630 - 160,881,158 (-)NCBI
RefSeq Acc Id: XM_054347564   ⟹   XP_054203539
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.03160,870,630 - 160,880,179 (-)NCBI
RefSeq Acc Id: XM_054347565   ⟹   XP_054203540
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.03160,870,630 - 160,879,743 (-)NCBI
RefSeq Acc Id: XM_054347566   ⟹   XP_054203541
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.03160,870,630 - 160,880,179 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_006875   ⟸   NM_006884
- Peptide Label: isoform a
- UniProtKB: O60467 (UniProtKB/Swiss-Prot),   O60465 (UniProtKB/Swiss-Prot),   O60903 (UniProtKB/Swiss-Prot),   O60902 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_003021   ⟸   NM_003030
- Peptide Label: isoform b
- UniProtKB: O60902 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001157150   ⟸   NM_001163678
- Peptide Label: isoform c
- UniProtKB: O60902 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006713790   ⟸   XM_006713727
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006713791   ⟸   XM_006713728
- Peptide Label: isoform X3
- UniProtKB: A6NLG4 (UniProtKB/TrEMBL),   C9J3D0 (UniProtKB/TrEMBL),   A0A0A0MSP8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016862542   ⟸   XM_017007053
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSP00000398704   ⟸   ENST00000425436
RefSeq Acc Id: ENSP00000374240   ⟸   ENST00000389589
RefSeq Acc Id: ENSP00000397099   ⟸   ENST00000441443
RefSeq Acc Id: ENSP00000419362   ⟸   ENST00000483851
RefSeq Acc Id: ENSP00000479329   ⟸   ENST00000554685
RefSeq Acc Id: XP_047304687   ⟸   XM_047448731
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054203538   ⟸   XM_054347563
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054203541   ⟸   XM_054347566
- Peptide Label: isoform X3
- UniProtKB: C9J3D0 (UniProtKB/TrEMBL),   A0A0A0MSP8 (UniProtKB/TrEMBL),   A6NLG4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_054203539   ⟸   XM_054347564
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054203540   ⟸   XM_054347565
- Peptide Label: isoform X2
Protein Domains
Homeobox   OAR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O60902-F1-model_v2 AlphaFold O60902 1-331 view protein structure

Promoters
RGD ID:6866108
Promoter ID:EPDNEW_H6219
Type:initiation region
Name:SHOX2_1
Description:short stature homeobox 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H6220  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,106,230 - 158,106,290EPDNEW
RGD ID:6866110
Promoter ID:EPDNEW_H6220
Type:initiation region
Name:SHOX2_2
Description:short stature homeobox 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H6219  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh383158,106,638 - 158,106,698EPDNEW
RGD ID:6801680
Promoter ID:HG_KWN:46561
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   Lymphoblastoid
Transcripts:UC003FBQ.1
Position:
Human AssemblyChrPosition (strand)Source
Build 363159,303,926 - 159,304,647 (-)MPROMDB
RGD ID:6801677
Promoter ID:HG_KWN:46562
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid
Transcripts:ENST00000389589,   UC003FBS.1,   UC010HVW.1
Position:
Human AssemblyChrPosition (strand)Source
Build 363159,306,221 - 159,307,627 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10854 AgrOrtholog
COSMIC SHOX2 COSMIC
Ensembl Genes ENSG00000168779 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000389589 ENTREZGENE
  ENST00000389589.8 UniProtKB/Swiss-Prot
  ENST00000441443 ENTREZGENE
  ENST00000441443.6 UniProtKB/Swiss-Prot
  ENST00000483851 ENTREZGENE
  ENST00000483851.7 UniProtKB/Swiss-Prot
  ENST00000490689 ENTREZGENE
  ENST00000554685.2 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000168779 GTEx
HGNC ID HGNC:10854 ENTREZGENE
Human Proteome Map SHOX2 Human Proteome Map
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HTH_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OAR_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:6474 UniProtKB/Swiss-Prot
NCBI Gene 6474 ENTREZGENE
OMIM 602504 OMIM
PANTHER SHORT STATURE HOMEOBOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SHORT STATURE HOMEOBOX PROTEIN 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA35756 PharmGKB
PRINTS HTHREPRESSR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WVB7_HUMAN UniProtKB/TrEMBL
  A0A0A0MSP8 ENTREZGENE
  A6NLG4 ENTREZGENE, UniProtKB/TrEMBL
  C9J3D0 ENTREZGENE
  O60465 ENTREZGENE
  O60467 ENTREZGENE
  O60902 ENTREZGENE
  O60903 ENTREZGENE
  SHOX2_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A0A0A0MSP8 UniProtKB/TrEMBL
  C9J3D0 UniProtKB/TrEMBL
  O60465 UniProtKB/Swiss-Prot
  O60467 UniProtKB/Swiss-Prot
  O60903 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-06-05 SHOX2  SHOX homeobox 2  SHOX2  short stature homeobox 2  Symbol and/or name change 19259463 PROVISIONAL