Shox2 (SHOX homeobox 2) - Rat Genome Database

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Gene: Shox2 (SHOX homeobox 2) Rattus norvegicus
Analyze
Symbol: Shox2
Name: SHOX homeobox 2 (Ensembl:short stature homeobox 2)
RGD ID: 3674
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 several processes, including heart development; positive regulation of cell development; and regulation of branching morphogenesis of a nerve. Predicted to act upstream of or within several processes, including positive regulation of cell population proliferation; regulation of transcription by RNA polymerase II; and skeletal system development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in lung cancer. Orthologous to human SHOX2 (SHOX homeobox 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: paired family homeodomain protein Prx3; short stature homeobox 2; short stature homeobox protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
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

Cellular Component
nucleus  (IBA,IEA)

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. 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.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
9. 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:9371788   PMID:16537395   PMID:17372176   PMID:17481601   PMID:18514492   PMID:21156168   PMID:22916278   PMID:23332764   PMID:26697824  


Genomics

Comparative Map Data
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
(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
(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
41 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:105
Count of miRNA genes:77
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000016843
Prediction methods:Miranda, 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
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1354594Despr10Despair related QTL 100.00000249locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)2114654253159654253Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
1582257Gluco21Glucose level QTL 213.10.0035blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2118111229157142209Rat
738007Anxrr7Anxiety related response QTL 74.4exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2118189491163189491Rat
1358360Sradr2Stress Responsive Adrenal Weight QTL 210.24adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)2129164097152195315Rat
6907363Bp357Blood pressure QTL 3574.10.002arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2129540907174540907Rat
1300165Rf9Renal function QTL 93.28kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)2133914684202447032Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)2135552573202446871Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2135552573202446871Rat
1298076Bp166Blood pressure QTL 1660.0009arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2136445150202447032Rat
1581502Esta3Estrogen-induced thymic atrophy QTL 3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2136916935189599348Rat
1359022Ppulsi1Prepulse inhibition QTL 13.63prepulse inhibition trait (VT:0003088)acoustic startle response measurement (CMO:0001519)2136916935213594495Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2141194931223265385Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2141194931223265385Rat
71113Cari2Carrageenan-induced inflammation QTL 22.70.009hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)2141596551202447032Rat
724568Uae13Urinary albumin excretion QTL 134.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)2143157029210020885Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2143657411190602963Rat
10043136Iddm54Insulin dependent diabetes mellitus QTL 543.40.0001blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2143657411190602963Rat
6903312Bw112Body weight QTL 1123.20.0013body mass (VT:0001259)body weight (CMO:0000012)2143657569184114274Rat
61401Niddm2Non-insulin dependent diabetes mellitus QTL 24.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2144599348189599348Rat
631520Bp73Blood pressure QTL 730.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147686913168355276Rat
1598833Bp295Blood pressure QTL 2953.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147798556192798556Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561221167075Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
1598805Memor8Memory QTL 83exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)2150341585189039377Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150341684202446871Rat
2301966Bp322Blood pressure QTL 3223.58arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2150540301202447032Rat
1354609Niddm62Non-insulin dependent diabetes mellitus QTL 624.720.000006insulin secretion trait (VT:0003564)plasma insulin level (CMO:0000342)2150540301202447032Rat

Markers in Region
D2Got333  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22151,223,786 - 151,223,949 (+)MAPPERmRatBN7.2
Rnor_6.02164,123,866 - 164,124,028NCBIRnor6.0
Rnor_5.02183,475,504 - 183,475,666UniSTSRnor5.0
RGSC_v3.42156,886,736 - 156,886,898UniSTSRGSC3.4
Celera2145,602,714 - 145,602,882UniSTS
Cytogenetic Map2q31UniSTS


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
Medium 4 30
Low 30 13 4 7 4 8 10 38 31 23 8 8
Below cutoff 1 7 11 7 9 7 1 4 4 15 1

Sequence


RefSeq Acc Id: ENSRNOT00000016843   ⟹   ENSRNOP00000016843
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2151,217,552 - 151,227,143 (-)Ensembl
Rnor_6.0 Ensembl2164,118,191 - 164,126,783 (-)Ensembl
RefSeq Acc Id: NM_013028   ⟹   NP_037160
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82153,527,571 - 153,537,161 (-)NCBI
mRatBN7.22151,217,552 - 151,227,143 (-)NCBI
Rnor_6.02164,118,175 - 164,126,783 (-)NCBI
Rnor_5.02183,469,813 - 183,478,421 (-)NCBI
RGSC_v3.42156,881,044 - 156,889,653 (-)RGD
Celera2145,597,026 - 145,605,637 (-)RGD
Sequence:
RefSeq Acc Id: XM_039101799   ⟹   XP_038957727
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82153,524,324 - 153,537,571 (-)NCBI
mRatBN7.22151,217,049 - 151,227,180 (-)NCBI
RefSeq Acc Id: NP_037160   ⟸   NM_013028
- UniProtKB: G3V7M9 (UniProtKB/TrEMBL),   A6J5K8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016843   ⟸   ENSRNOT00000016843
RefSeq Acc Id: XP_038957727   ⟸   XM_039101799
- Peptide Label: isoform X1
- UniProtKB: A6J5K7 (UniProtKB/TrEMBL)
Protein Domains
Homeobox   OAR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35750-F1-model_v2 AlphaFold O35750 1-237 view protein structure

Transcriptome

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

Promoters
RGD ID:13691363
Promoter ID:EPDNEW_R1888
Type:single initiation site
Name:Shox2_1
Description:short stature homeobox 2
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_6.02164,126,708 - 164,126,768EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3674 AgrOrtholog
BioCyc Gene G2FUF-52872 BioCyc
Ensembl Genes ENSRNOG00000012478 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016843 ENTREZGENE
  ENSRNOT00000016843.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 rno:25546 UniProtKB/Swiss-Prot
NCBI Gene 25546 ENTREZGENE
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
PhenoGen Shox2 PhenoGen
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
RatGTEx ENSRNOG00000012478 RatGTEx
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC228946
UniProt A6J5K7 ENTREZGENE, UniProtKB/TrEMBL
  A6J5K8 ENTREZGENE, UniProtKB/TrEMBL
  A6J5K9_RAT UniProtKB/TrEMBL
  G3V7M9 ENTREZGENE, UniProtKB/TrEMBL
  O35750 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O35749 UniProtKB/Swiss-Prot
  O35751 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-06-09 Shox2  SHOX homeobox 2  Shox2  short stature homeobox 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Shox2  Short stature homeobox 2      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_process human homolog encodes putative homeobox gene involved in embryonic development 704404