GSC2 (goosecoid homeobox 2) - Rat Genome Database

Name: GSC2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: GSC2 (goosecoid homeobox 2) Chlorocebus sabaeus

Analyze

Symbol:

GSC2

Name:

goosecoid homeobox 2

RGD ID:

18699172

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN regulation of transcription by RNA polymerase II (ortholog); ASSOCIATED WITH autism spectrum disorder (ortholog); autistic disorder (ortholog); chromosome 22q11.2 deletion syndrome, distal (ortholog); FOUND IN nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein goosecoid-2

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	GSC2 (goosecoid homeobox 2)	NCBI	Ortholog
Mus musculus (house mouse):	Gsc2 (goosecoid homebox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Gsc2 (goosecoid homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Gsc2 (goosecoid homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	GSC2 (goosecoid homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	GSC2 (goosecoid homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Gsc2 (goosecoid homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	GSC2 (goosecoid homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Gsc2 (goosecoid homeobox 2)	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
ChlSab1.1	19	6,598,246 - 6,601,230 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	19	6,598,259 - 6,599,532 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666085	331,282 - 334,587 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

autistic disorder (ISO)

chromosome 22q11.2 deletion syndrome, distal (ISO)

chromosome 22q11.2 microduplication syndrome (ISO)

DiGeorge syndrome (ISO)

epilepsy (ISO)

genetic disease (ISO)

immunodeficiency 51 (ISO)

intellectual disability (ISO)

megacolon (ISO)

Neurodevelopmental Disorders (ISO)

Polyarteritis Nodosa, Childhood-Onset (ISO)

primary immunodeficiency disease (ISO)

schizophrenia (ISO)

velocardiofacial syndrome (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA,ISO)

Cellular Component

nucleus (IEA)

Molecular Function

DNA binding (IEA)

DNA-binding transcription factor activity (IEA)

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

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

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

GSC2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	19	6,598,246 - 6,601,230 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	19	6,598,259 - 6,599,532 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666085	331,282 - 334,587 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

GSC2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	22	19,146,993 - 19,150,292 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	22	19,146,993 - 19,150,292 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	22	19,134,506 - 19,137,805 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	22	17,516,504 - 17,517,796 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	22	17,511,057 - 17,512,350	NCBI
Celera	22	2,988,450 - 2,989,742 (-)	NCBI		Celera
Cytogenetic Map	22	q11.21	NCBI
CHM1_1	22	19,136,007 - 19,137,299 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	22	19,521,533 - 19,524,832 (-)	NCBI		T2T-CHM13v2.0

Gsc2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	16	17,730,978 - 17,732,891 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	16	17,730,971 - 17,732,923 (-)	Ensembl		GRCm39 Ensembl
GRCm38	16	17,913,114 - 17,915,027 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	16	17,913,107 - 17,915,059 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	16	17,913,647 - 17,915,152 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
Celera	16	18,486,619 - 18,488,124 (-)	NCBI		Celera
Cytogenetic Map	16	A3	NCBI
cM Map	16	11.1	NCBI

Gsc2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	11	96,576,424 - 96,578,412 (+)	NCBI		GRCr8
mRatBN7.2	11	83,070,784 - 83,075,874 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	11	83,072,138 - 83,074,126 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	11	91,800,750 - 91,802,738 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	11	84,461,884 - 84,463,872 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	11	83,515,499 - 83,517,487 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	11	87,220,618 - 87,222,606 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	11	87,220,618 - 87,222,606 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	11	90,312,181 - 90,314,169 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	11	85,060,271 - 85,062,259 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	11	85,100,906 - 85,102,374 (+)	NCBI
Celera	11	81,848,147 - 81,850,135 (+)	NCBI		Celera
Cytogenetic Map	11	q23	NCBI

Gsc2
(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_004955442	18,823,495 - 18,825,760 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955442	18,824,187 - 18,825,760 (+)	NCBI	ChiLan1.0	ChiLan1.0

GSC2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	23	28,766,957 - 28,770,180 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	22	31,314,549 - 31,317,772 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	22	1,901,389 - 1,904,671 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	22	17,581,449 - 17,584,239 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

GSC2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	26	30,033,185 - 30,034,174 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	26	29,987,283 - 29,988,471 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	26	31,433,426 - 31,437,346 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	26	31,434,465 - 31,436,086 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	26	29,482,654 - 29,485,525 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	26	29,106,059 - 29,108,277 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	26	30,193,559 - 30,198,109 (+)	NCBI		UU_Cfam_GSD_1.0

Gsc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405118	139,595,069 - 139,599,230 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936619	3,157,228 - 3,174,086 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936619	3,154,834 - 3,158,654 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

GSC2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	50,957,991 - 50,960,193 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	50,956,315 - 50,960,424 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	54,523,278 - 54,527,379 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Gsc2
(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_004624945	172,345 - 176,191 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624945	172,345 - 176,453 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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

	endocrine system	hemolymphoid system	nervous system
High
Medium
Low		9
Below cutoff	3	8	22

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_007975067	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_007975068	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000053	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000009583 ⟹ ENSCSAP00000007694

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	19	6,598,259 - 6,599,532 (+)	Ensembl

RefSeq Acc Id:

XM_007975068 ⟹ XP_007973259

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	19	6,598,246 - 6,601,230 (+)	NCBI
Vero_WHO_p1.0	NW_023666085	331,282 - 334,587 (-)	NCBI

Sequence:

show sequence

GGCCGGGCAGGGCATGGCGGCAGCGGCGGGGGGCGCGGCGAGCCGCCGGGGCCCCGGGCGGCCC
TGCCCCTTCTCCATCGAGCACATCCTCTCCAGCCTGCCCGAGCGGAGCCTCCCGGCCCGGGCCG
CCTGCCCACCGCAGCCCGCCGGTGGCCAGAGCCCCACCGAACCAGAGGAGCCCGGGGCGCCCGA
GGCTGCGCCTTGCGCCTGCTGTTGCTGCTGCAGCCCCCGCGCGGGGCCCTGCGGGCCCCCAGAG
GCGGCAGCCGGGCTGAGCGCTCGTCTGGCGTGGCCGCTGAGGCTGGGACCCGCGGTGCCCTTGT
CCTTGGGTGCGCCAGCTGGAGGTTCCGGGGCGCTCCCGGGCCCGGTCGGCCCGGGTTCGCAGCG
GCGCACGCGGCGCCACCGCACCATCTTCAGCGAGGAGCAGCTGCAGGCGCTCGAGGCGCTCTTC
GTGCAGAACCAGTATCCTGACGTGAGCACGCGCGAGCGCCTGGCCGGCCGCATCCGCCTTCGCG
AGGAGCGCGTGGAGGTCTGGTTCAAGAACCGCCGGGCCAAATGGCGACACCAGAAGCGCGCGTC
GGCTTCCGCGAGGCTCCTGCCCGGCGTCAAGAAGTCCTCCAAGGGGAGCTGCTGATGACTCTAG
GAGCTGCCCCTGGGCTCGGCCACCCTTTTTGGGATCTTTGGAGTTGGCGCTGAGAGAAGACAGA
TCTACCCGAAAAGGAGCTAGGAGAGTACACCCGTCTGCTCCGCCCGTCTCCACAGCCCTTGCCT
CCTGCAGCTCGTACCCTAAAGACAGCTGTACCCTAAACACTCCTCGCTGGGAAGGAAGGACCGC
AGCCCAGGGCCCCCGGTGCATGGTGTTCCACGGTAGTGGGAGTGGAGAGTCCCTTGGGGGTGGG
CTGGGGCATAGAACAGCTTCCTCACCCCCTCATCACCCCAAGAGACACTAACTCTACCCCAGGA
AGGAACCACGCCGTATCAACACTGGCCCCAGAATCCTCCGCAGTGGAGCCTCTCTCCGCACCCT
GGGACATGCTGGCCTCCCTCTTCTCAATGTGGACGTTGACCCAACTTGACCTGGCCCGCCCTCC
CCCAGCGGGAAGCGGGGTGGGGTTCGTGTCTGTGCAGTCCTGGGATTGCAGGCTTCCCAGACCC
TGGGCTGACTCTTGGTATCTGGGCCTGTAGGATAAGAAGGTCGCAGGAGCGATTCCAGGAGCCC
CTCCCGAGTCCCTTGACCTTCGAGCCTCGCGCTGATACTGAGAAACAAGCAACTTCAGATACCA
CAGAAGCCGCCCAGAGTCTCAAGTCCACCTTGGCTCCACCCTCACAACCAACAAGGAGCTGTCC
CTTCTCCTTCCTTCCCAGTGAGGGGTGTTTAGGGTACAGCTGTCTTTGAGAGGAGCACAGCTTA
GCGAGGCCTCAGTCTCTGCACCAGGGTGCTCCCCAGCAGAGGAGACTGCTCCATAGATGGTGGC
CTTGGGCCCCTGGGATCCAGCCCTGGCCTCTGGGCTACCGTGAACCTGCCCATGGGTGGGGGTC
CCCTGCTTCCTCCTGGGGTTTTCATGCTGTGGGGTCGGCCTGCCTCACAGCAATCTCTGCCGTC
CTAGGGTAGGGCAAGAGGAGGTTGGATTGGGGAGACCCCACCCCTGCTGCCTAGGAAGATGCCT
GCCCTCCCCTTCTTTATCCTGGCCCATGGCGAAAGGCACCGTGGAAAGAAGCCTTCGATTCTCC
AAGTAGGCCCTACAGTGGGTCCAAAGCATCTCACATCCCCTTCAGCTGGCTTGAGCACCTCGAT
CTGTCTCCTTACAGGCCCTGCAGGAAACGGGGCAGTTCTACCTGCAGGAGACGAAATCCATCTC
TAAAAGCAGGACTGCAAAAGCCAGGGCTGCAGCTCCTCGGACACCCCAAGGCTGGCCAGCTTGG
ATAACACCAAGCAAGCATGGTGTCCCCAGTCAGAACTGCCCTGACACTGCTGGGTGTCCCTAGC
ATCCCCGCCTCCACCCCTAGCATGCACACTGCTGGTTGTCACAAAACCCTTCTCCCCGAACCCT
GGTCTTGCCCTTGGGGACTGAACAGACTACCTGTGGACATGCCCGTGTCCCGGTCAGCTCCCTT
GCAGGTGGAGACACTCCCATCTGGCGGGCTCCGGGCTCCGGGCTCCTCGCACTCCTTGGTTGAA
TGGCCATCTGTCATCGTGTTGGGAGCCCTGATCAGAGCTTGTGGAGCGCCACCTTCCAGGGCTC
AGTGGCTGTGTTGCTCTCCTGAATTTGCTCCTTGAGCTCTAGCTGCTCCTTGGCAGGCCGACCC
CCCACAGCAGGCTGTTAACATAGGC

hide sequence

Protein Sequences


Protein RefSeqs	XP_007973259	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000007694
	ENSCSAP00000007694.1

RefSeq Acc Id:	XP_007973259 ⟸ XM_007975068
- UniProtKB:	A0A0D9RGF5 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000007694 ⟸ ENSCSAT00000009583

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000011500	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000009583.1	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
NCBI Gene	GSC2	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN GOOSECOID-2	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN GOOSECOID-RELATED	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	A0A0D9RGF5	ENTREZGENE, UniProtKB/TrEMBL

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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