SHOX (SHOX homeobox) - Rat Genome Database

Name: SHOX
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: SHOX (SHOX homeobox) Chlorocebus sabaeus

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Symbol:

SHOX

Name:

SHOX homeobox

RGD ID:

18363489

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN positive regulation of transcription by RNA polymerase II (inferred); regulation of DNA-templated transcription (inferred); regulation of transcription by RNA polymerase II (inferred); ASSOCIATED WITH autistic disorder (ortholog); connective tissue disease (ortholog); Langer Mesomelic Dysplasia (ortholog); FOUND IN intracellular membrane-bounded organelle (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

short stature homeobox; short stature homeobox protein

RGD Orthologs

Alliance Orthologs

More Info

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More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SHOX (SHOX homeobox)	NCBI	Ortholog
Mus musculus (house mouse):	Rhox10 (reproductive homeobox 10)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Shox1 (SHOX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Shox (SHOX homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SHOX (SHOX homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SHOX (SHOX homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Shox (SHOX homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChlSab1.1 - Green Monkey 1.1 Assembly

Position:

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Vero_WHO_p1.0	NW_023666056	452,707 - 466,430 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

connective tissue disease (ISO)

Langer Mesomelic Dysplasia (ISO)

Leri-Weill dyschondrosteosis (ISO)

schizophrenia (ISO)

SHOX-related short stature (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

positive regulation of transcription by RNA polymerase II (IEA)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA)

Cellular Component

intracellular membrane-bounded organelle (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription activator activity, RNA polymerase II-specific (IEA)

DNA-binding transcription factor activity, RNA polymerase II-specific (IEA)

protein binding (ISO)

sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

SHOX
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Vero_WHO_p1.0	NW_023666056	452,707 - 466,430 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

SHOX
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	Y	624,344 - 659,411 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38	X	624,344 - 659,411 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	624,344 - 659,411 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p14 Ensembl	Y	624,344 - 659,411 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	Y	535,079 - 570,146 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	X	585,079 - 620,146 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	Y	505,079 - 540,146 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 36	X	505,079 - 540,146 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	Y	555,078 - 590,146	NCBI
Celera	X	471,885 - 506,319 (-)	NCBI		Celera
Cytogenetic Map	X	;Y	NCBI
CHM1_1	X	568,610 - 603,454 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	X	464,175 - 499,150 (+)	NCBI		T2T-CHM13v2.0
T2T-CHM13v2.0	Y	478,002 - 512,484 (+)	NCBI		T2T-CHM13v2.0

Rhox10
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	37,155,352 - 37,160,565 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	37,155,352 - 37,160,568 (+)	Ensembl		GRCm39 Ensembl
GRCm38	X	38,066,475 - 38,071,688 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	38,066,475 - 38,071,691 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	35,419,652 - 35,424,865 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	X	34,311,102 - 34,316,301 (+)	NCBI		MGSCv36	mm8
Celera	X	25,712,038 - 25,717,251 (+)	NCBI		Celera
Cytogenetic Map	X	A3.3	NCBI
cM Map	X	22.32	NCBI

Shox1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	121,553,770 - 121,560,788 (-)	NCBI		GRCr8
mRatBN7.2	X	116,688,163 - 116,695,111 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	116,688,163 - 116,695,058 (-)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	X	124,045,727 - 124,052,708 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	124,045,737 - 124,052,632 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	124,131,979 - 124,138,919 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	7,446,404 - 7,453,299 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	X	115,912,706 - 115,919,422 (-)	NCBI		Celera
Cytogenetic Map	X	q35	NCBI

Shox
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955499	716,362 - 729,008 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955499	716,476 - 725,455 (+)	NCBI	ChiLan1.0	ChiLan1.0

SHOX
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	414,862 - 424,071 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	414,039 - 424,109 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	353,022 - 362,230 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	X	320,382 - 329,593 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	X	319,900 - 329,631 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	X	314,181 - 323,381 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	X	328,176 - 337,382 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	X	326,737 - 335,948 (+)	NCBI		UU_Cfam_GSD_1.0

SHOX
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa10.2	X	554,736 - 566,761 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Shox
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624834	391,912 - 399,180 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624834	391,912 - 399,180 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_008019614	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000024	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_008019614 ⟹ XP_008017805

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
Vero_WHO_p1.0	NW_023666056	452,707 - 466,430 (+)	NCBI

Sequence:

show sequence

CCACCCCCGGCCCCCAGCCATGGAAGAACTCACGGCGTTTGTCTCCAAGTCTTTTGACCAGAAA
AGCAAGGACGGTAACGGCGGAGGCGGCGGCGGCGGAGGGAAGAAGGATTCCATTACGTACCGGG
AAGTTTTGGAGAGCGGACTGGCGCGCTCCCGGGAGCTGGGGACGTCCGATTCCAGCCTCCAGGA
CCTCGCGGAGGGCGGCGGCCACTGCCCGGTGCATTTGTTCAAGGACCACGTAGACAATGACAAG
GAGAAACTGAAAGAATTCGGCGCCGGGAGAGTGGCGGAAGGGATTTACGAATGCAAAGAGAAGC
GCGAGGACGTGAAGTCGGAGGACGAGGACGGGCAGACGAAGCTGAAACAGAGGCGCAGCCGCAC
CAACTTCACGCTGGAGCAGCTGAACGAGCTGGAGCGACTCTTCGACGAGACCCATTACCCCGAC
GCCTTCATGCGCGAGGAGCTCAGCCAGCGCCTGGGGCTTTCCGAGGCGCGCGTGCAGGTTTGGT
TCCAGAACCGGAGAGCCAAGTGCCGCAAACAGGAGAATCAGATGCATAAAGGCGTCATCTTAGG
CACAGCCAACCACCTGGACGCCTGCCGGGTGGCACCCTACGTGAACATGGGAGCCTTAAGGATG
CCTTTTCAACAGGTCCAGGCTCAGCTGCAGCTGGAAGGCGTGGCCCACGCGCACCCGCACCTGC
ACCCGCACCTGGCGGCGCACGCGCCCTACCTGATGTTCCCCCCGCCGCCCTTCGGGCTGCCCAT
CGCGTCGCTGGCCGAGTCCGCCTCGGCCGCCGCCGTGGTCGCCGCCGCGGCCAAGAGCAACAGC
AAAAACTCCAGCATCGCCGACCTGCGGCTCAAGGCGCGGAAGCACGCGGAGGCCTTGGGGCTCT
GACCCCGCCGCGCAGCCCCCAGCGCACCGGGACTCCCGGGCTCCGCGCACCCCGCCTGCACCGC
GCGTTCTGCACT

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Protein Sequences


Protein RefSeqs	XP_008017805	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000014384.1

RefSeq Acc Id:	XP_008017805 ⟸ XM_008019614
- UniProtKB:	A0A0D9S0J5 (UniProtKB/TrEMBL)

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000018374	UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000016475.1	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	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	csab:103247477	UniProtKB/TrEMBL
NCBI Gene	SHOX	ENTREZGENE
PANTHER	SHORT STATURE HOMEOBOX	UniProtKB/TrEMBL
	SHORT STATURE HOMEOBOX PROTEIN	UniProtKB/TrEMBL
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	A0A0D9S0J5	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2023-06-13	SHOX	SHOX homeobox	SHOX	short stature homeobox	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - OMIM