LHX5 (LIM homeobox 5) - Rat Genome Database

Name: LHX5
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: LHX5 (LIM homeobox 5) Chlorocebus sabaeus

Analyze

Symbol:

LHX5

Name:

LIM homeobox 5

RGD ID:

18390531

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); metal ion binding (inferred); INVOLVED IN cell proliferation in forebrain (ortholog); cell-cell signaling (ortholog); cerebellar Purkinje cell differentiation (ortholog); ASSOCIATED WITH genetic disease (ortholog); FOUND IN nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

LIM/homeobox protein Lhx5

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):	LHX5 (LIM homeobox 5)	NCBI	Ortholog
Mus musculus (house mouse):	Lhx5 (LIM homeobox protein 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Lhx5 (LIM homeobox 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Lhx5 (LIM homeobox 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	LHX5 (LIM homeobox 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LHX5 (LIM homeobox 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Lhx5 (LIM homeobox 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	LHX5 (LIM homeobox 5)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Lhx5 (LIM homeobox 5)	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	11	108,718,452 - 108,727,156 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	108,718,925 - 108,727,139 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	136,366,070 - 136,376,140 (+)	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

genetic disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell proliferation in forebrain (IEA,ISO)

cell-cell signaling (IEA,ISO)

cerebellar Purkinje cell differentiation (IEA,ISO)

cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (IEA,ISO)

cerebellum development (IEA,ISO)

forebrain neuron differentiation (IEA,ISO)

hippocampus development (IEA,ISO)

neuroblast proliferation (IEA,ISO)

neuron differentiation (IEA)

positive regulation of DNA-templated transcription (IEA)

regulation of DNA-templated transcription (IEA)

regulation of neuroblast proliferation (IEA,ISO)

regulation of transcription by RNA polymerase II (IEA)

spinal cord association neuron differentiation (IEA)

Cellular Component

nucleus (IEA)

Molecular Function

DNA binding (IEA)

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

metal ion binding (IEA)

protein binding (ISO)

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

sequence-specific double-stranded DNA binding (IEA)

zinc ion binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

LHX5
(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	11	108,718,452 - 108,727,156 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	108,718,925 - 108,727,139 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	136,366,070 - 136,376,140 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

LHX5
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	113,462,033 - 113,471,871 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	113,462,033 - 113,472,280 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	113,899,838 - 113,909,676 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	112,385,077 - 112,394,260 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	112,363,413 - 112,372,597	NCBI
Celera	12	113,527,582 - 113,536,765 (-)	NCBI		Celera
Cytogenetic Map	12	q24.13	NCBI
HuRef	12	110,911,297 - 110,920,482 (-)	NCBI		HuRef
CHM1_1	12	113,868,362 - 113,877,545 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	12	113,438,040 - 113,447,878 (-)	NCBI		T2T-CHM13v2.0

Lhx5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	120,569,951 - 120,579,522 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	120,569,764 - 120,579,288 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	120,431,886 - 120,441,457 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	120,431,699 - 120,441,223 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	120,881,895 - 120,891,466 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	120,692,518 - 120,702,074 (+)	NCBI		MGSCv36	mm8
Celera	5	117,516,048 - 117,525,759 (+)	NCBI		Celera
Cytogenetic Map	5	F	NCBI
cM Map	5	60.62	NCBI

Lhx5
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	12	41,786,746 - 41,795,183 (-)	NCBI		GRCr8
mRatBN7.2	12	36,126,186 - 36,134,625 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	12	36,126,186 - 36,134,625 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	12	37,305,452 - 37,313,885 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	12	37,916,669 - 37,925,101 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	12	36,969,146 - 36,977,578 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	12	41,663,000 - 41,671,437 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	12	41,663,000 - 41,671,437 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	12	43,513,076 - 43,521,513 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	12	37,323,820 - 37,332,257 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	12	37,187,214 - 37,195,645 (-)	NCBI
Celera	12	37,784,186 - 37,792,623 (-)	NCBI		Celera
Cytogenetic Map	12	q16	NCBI

Lhx5
(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_004955482	9,682,526 - 9,691,530 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955482	9,682,671 - 9,691,155 (-)	NCBI	ChiLan1.0	ChiLan1.0

LHX5
(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	10	121,544,899 - 121,557,434 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	121,541,297 - 121,553,833 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	111,063,466 - 111,075,445 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	114,445,759 - 114,454,960 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	114,445,766 - 114,454,960 (-)	Ensembl	panpan1.1		panPan2

LHX5
(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	10,776,991 - 10,785,820 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	26	10,777,242 - 10,785,815 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	26	10,901,082 - 10,909,374 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	26	11,027,504 - 11,035,796 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	26	11,026,813 - 11,035,727 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	26	10,996,951 - 11,005,243 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	26	11,059,577 - 11,067,865 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	26	11,108,837 - 11,117,131 (-)	NCBI		UU_Cfam_GSD_1.0

Lhx5
(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	148,746,922 - 148,756,459 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936668	3,246,456 - 3,255,353 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936668	3,246,456 - 3,255,353 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

LHX5
(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	38,446,899 - 38,456,404 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	38,446,781 - 38,456,460 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	40,911,815 - 40,920,132 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

Lhx5
(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_004624747	19,088,311 - 19,097,080 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624747	19,088,372 - 19,097,406 (+)	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

	hemolymphoid system	nervous system
High
Medium
Low	11
Below cutoff	7	2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_008004831	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JACDXN010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCSAT00000000373 ⟹ ENSCSAP00000015683

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1 Ensembl	11	108,718,925 - 108,727,139 (-)	Ensembl

RefSeq Acc Id:

XM_008004831 ⟹ XP_008003022

Type:

CODING

Position:

Green Monkey Assembly	Chr	Position (strand)	Source
ChlSab1.1	11	108,718,452 - 108,727,156 (-)	NCBI
Vero_WHO_p1.0	NW_023666037	136,366,070 - 136,376,140 (+)	NCBI

Sequence:

show sequence

CGCCGGGGCACGCGGCTATGATGGTGCACTGTGCCGGTTGCGAGCGGCCCATCCTCGACCGCTT
TCTGCTGAACGTACTGGACCGCGCGTGGCACATCAAATGTGTTCAGTGCTGCGAGTGCAAAACC
AATCTCTCGGAGAAGTGCTTCTCGCGCGAGGGCAAGCTCTACTGCAAAAATGACTTCTTCAGGC
GCTTTGGCACCAAATGCGCTGGCTGCGCGCAAGGCATCTCGCCCAGCGACCTGGTGCGCAAGGC
CCGGAGCAAAGTCTTTCACCTCAACTGTTTCACCTGCATGGTGTGTAACAAGCAGCTGTCCACC
GGCGAGGAGCTCTACGTCATCGACGAGAACAAGTTCGTGTGCAAAGACGACTACCTGAGCTCAT
CCAGCCTCAAGGAGGGCAGCCTCAACTCAGTATCATCCTGTACGGACCGCAGTTTGTCCCCGGA
CCTCCAGGACGCACTGCAGGACGACCCCAAGGAGACGGACAACTCGACCTCGTCGGACAAGGAG
ACGGCCAACAACGAGAACGAGGAGCAGAACTCGGGCACCAAGCGGCGCGGCCCGCGCACCACCA
TAAAGGCCAAGCAGCTGGAGACGCTCAAGGCTGCCTTCGCCGCCACGCCCAAGCCCACGCGCCA
CATCCGCGAGCAGCTGGCGCAGGAGACCGGCCTCAACATGCGCGTCATCCAGGTGTGGTTTCAG
AACCGACGGTCCAAAGAACGCCGGATGAAACAGTTGAGCGCCCTGGGCGCCCGGAGGCACGCCT
TCTTCCGGAGTCCGCGGCGCATGCGTCCGCTGGGCGGCCGCTTGGACGAGTCTGAGATGTTGGG
GTCCACCCCGTACACCTATTATGGAGACTACCAAGGTGACTACTATGCTCCGGGAAGCAACTAC
GACTTCTTCGCTCACGGCCCGCCTTCGCAGGCGCAGTCCCCGGCCGACTCCAGCTTCCTGGCGG
CCTCGGGCCCCGGCTCTACGCCGCTGGGCGCGCTGGAGCCGCCGCTCGCTGGCCCGCACGCCGC
AGACAACCCCAGGTTCACCGACATGATCTCGCACCCGGACACGCCGAGCCCCGAGCCGGGCCTG
CCGGGCGCGCTGCACCCCATGCCCGGCGAGGTGTTCAGCGGCGGGCCCAGCCCGCCCTTCCCCA
TGAGCGGCACCAGCGGCTATAGCGGACCCCTGTCGCATCCCAACCCGGAGCTCAACGAGGCCGC
CGTGTGGTAAGGCCGCCGGGCCGCCCCCCGCGCTCGGTCCCCGGGGGCCCCGCCCCGAAGCAAC
CTCCTGAAACCAAAACGCCCGACGCGGACACGGTGGGAGATGTGGGTATTCCTCGGGGGTTCTC
TCTCGGGTCCGCACTCAACTGGCAGCTGCTCCTCGGCTGGACGCCGAGGGGGGCCGACCCCCAT
CTCCACTTCACGGGCTCTCCAGGGGCCTCAGCCCACCGCCAGCACTCTCCCGGCAACCGCGAGC
AATTTCTTGGGACCAAAGTCAATACTCCGGAGGGTCAAGAGATTTTGAGCACGCTCTAGACTTT
CCCGGGGCCCCCACCCACCCACTCAGCCACCGCCACCTTTTTGGACTGAGAGAGGGTGAGGCCA
AGAGGCGGAGACGGTGTTATTCCCTCTCTCTGCAATCCGAGGGGCATTTTGTAACCTTATTTCT
CGCTGTGCTTAGTCTGTCTCAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_008003022	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCSAP00000015683
	ENSCSAP00000015683.1

RefSeq Acc Id:	XP_008003022 ⟸ XM_008004831
- UniProtKB:	A0A0D9S494 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSCSAP00000015683 ⟸ ENSCSAT00000000373

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCSAG00000002361	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCSAT00000000373.1	UniProtKB/TrEMBL
Gene3D-CATH	Cysteine Rich Protein	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Lhx1/5_LIM1	UniProtKB/TrEMBL
	Lhx1/5_LIM2	UniProtKB/TrEMBL
	Znf_LIM	UniProtKB/TrEMBL
KEGG Report	csab:103239173	UniProtKB/TrEMBL
NCBI Gene	LHX5	ENTREZGENE
PANTHER	LIM/HOMEOBOX PROTEIN LHX	UniProtKB/TrEMBL
	LIM/HOMEOBOX PROTEIN LHX5	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
	LIM	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
	LIM_DOMAIN_1	UniProtKB/TrEMBL
	LIM_DOMAIN_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
	LIM	UniProtKB/TrEMBL
Superfamily-SCOP	Glucocorticoid receptor-like (DNA-binding domain)	UniProtKB/TrEMBL
	SSF46689	UniProtKB/TrEMBL
UniProt	A0A0D9S494	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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