Lhx6 (LIM homeobox 6) - Rat Genome Database

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Gene: Lhx6 (LIM homeobox 6) Chinchilla lanigera
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Symbol: Lhx6
Name: LIM homeobox 6
RGD ID: 8758910
Description: ENCODES a protein that exhibits sequence-specific double-stranded DNA binding (ortholog); INVOLVED IN cerebral cortex GABAergic interneuron migration (ortholog); cerebral cortex neuron differentiation (ortholog); cerebral cortex radially oriented cell migration (ortholog); FOUND IN nucleus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LIM/homeobox protein Lhx6
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554195,834,547 - 5,858,113 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554195,835,230 - 5,858,096 (+)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISO annotations across species
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Lhx6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554195,834,547 - 5,858,113 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554195,835,230 - 5,858,096 (+)NCBIChiLan1.0ChiLan1.0
LHX6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389122,202,582 - 122,228,957 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9122,202,577 - 122,229,626 (-)EnsemblGRCh38hg38GRCh38
GRCh379124,964,861 - 124,991,236 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369124,004,679 - 124,030,840 (-)NCBINCBI36Build 36hg18NCBI36
Celera995,613,158 - 95,639,326 (-)NCBICelera
Cytogenetic Map9q33.2NCBI
HuRef994,579,638 - 94,605,760 (-)NCBIHuRef
CHM1_19125,112,910 - 125,139,147 (-)NCBICHM1_1
T2T-CHM13v2.09134,400,069 - 134,426,451 (-)NCBIT2T-CHM13v2.0
Lhx6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39235,971,962 - 35,996,004 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl235,971,965 - 35,995,420 (-)EnsemblGRCm39 Ensembl
GRCm38236,081,950 - 36,105,992 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl236,081,953 - 36,105,408 (-)EnsemblGRCm38mm10GRCm38
MGSCv37235,937,473 - 35,960,928 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36235,905,548 - 35,927,280 (-)NCBIMGSCv36mm8
Celera235,785,674 - 35,809,139 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map224.17NCBI
Lhx6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8339,829,846 - 39,853,681 (-)NCBIGRCr8
mRatBN7.2319,432,439 - 19,456,268 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl319,433,494 - 19,456,061 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx322,510,924 - 22,534,512 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0331,095,849 - 31,119,442 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0329,343,118 - 29,366,747 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0315,409,349 - 15,433,504 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl315,411,939 - 15,433,252 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0320,718,972 - 20,742,583 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4315,192,524 - 15,216,076 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1315,088,870 - 15,113,701 (-)NCBI
Celera314,144,852 - 14,168,405 (-)NCBICelera
Cytogenetic Map3p11NCBI
LHX6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21117,117,476 - 17,172,379 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1917,119,825 - 17,174,732 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0993,303,447 - 93,353,896 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19121,668,585 - 121,693,605 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9121,670,707 - 121,694,378 (-)Ensemblpanpan1.1panPan2
LHX6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1960,348,529 - 60,374,037 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl960,348,335 - 60,374,024 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha959,543,996 - 59,581,491 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0961,263,724 - 61,301,199 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl961,263,679 - 61,289,115 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1960,037,892 - 60,075,327 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0960,354,214 - 60,391,774 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0960,442,894 - 60,480,404 (+)NCBIUU_Cfam_GSD_1.0
Lhx6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947190,823,007 - 190,847,434 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648710,591,532 - 10,616,017 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648710,591,532 - 10,616,017 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LHX6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1262,295,353 - 262,322,530 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11262,297,557 - 262,322,777 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21294,597,333 - 294,622,577 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LHX6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11217,364,693 - 17,392,756 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1217,366,826 - 17,386,276 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603525,656,604 - 25,683,197 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lhx6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476013,066,703 - 13,097,468 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476013,066,632 - 13,092,006 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSCLAT00000018730   ⟹   ENSCLAP00000018548
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554195,834,547 - 5,858,113 (+)Ensembl
Ensembl Acc Id: ENSCLAT00000018731   ⟹   ENSCLAP00000018549
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554195,835,230 - 5,855,992 (+)Ensembl
Ensembl Acc Id: ENSCLAT00000018732   ⟹   ENSCLAP00000018550
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554195,835,233 - 5,851,998 (+)Ensembl
RefSeq Acc Id: XM_005382538   ⟹   XP_005382595
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554195,835,230 - 5,858,096 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005382540   ⟹   XP_005382597
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554195,835,230 - 5,856,366 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013513079   ⟹   XP_013368533
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554195,835,230 - 5,858,096 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013513080   ⟹   XP_013368534
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554195,835,230 - 5,856,366 (+)NCBI
Sequence:
RefSeq Acc Id: XM_013513081   ⟹   XP_013368535
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554195,835,230 - 5,856,366 (+)NCBI
Sequence:
RefSeq Acc Id: XP_005382597   ⟸   XM_005382540
- Peptide Label: isoform X4
- UniProtKB: A0A8C2VRE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005382595   ⟸   XM_005382538
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_013368533   ⟸   XM_013513079
- Peptide Label: isoform X2
- UniProtKB: A0A8C2VRE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013368534   ⟸   XM_013513080
- Peptide Label: isoform X3
- UniProtKB: A0A8C2VRE5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_013368535   ⟸   XM_013513081
- Peptide Label: isoform X5
- UniProtKB: A0A8C2VWI2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSCLAP00000018548   ⟸   ENSCLAT00000018730
Ensembl Acc Id: ENSCLAP00000018549   ⟸   ENSCLAT00000018731
Ensembl Acc Id: ENSCLAP00000018550   ⟸   ENSCLAT00000018732
Protein Domains
Homeobox   LIM zinc-binding


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000012726 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000018730 ENTREZGENE
  ENSCLAT00000018730.1 UniProtKB/TrEMBL
  ENSCLAT00000018731 ENTREZGENE
  ENSCLAT00000018731.1 UniProtKB/TrEMBL
  ENSCLAT00000018732.1 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
  LIM_Homeobox_TF UniProtKB/TrEMBL
  Znf_LIM UniProtKB/TrEMBL
NCBI Gene Lhx6 ENTREZGENE
PANTHER LIM/HOMEOBOX PROTEIN LHX UniProtKB/TrEMBL
  LIM/HOMEOBOX PROTEIN LHX6 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 A0A8C2VRE5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C2VTB5_CHILA UniProtKB/TrEMBL
  A0A8C2VWI2 ENTREZGENE, UniProtKB/TrEMBL