Human Gene LHX6 (uc004blx.4)
Description: Homo sapiens LIM homeobox 6 (LHX6), transcript variant 1, mRNA.
RefSeq Summary (NM_014368): This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017].
Transcript (Including UTRs)
Position: hg19 chr9:124,964,856-124,991,091 Size: 26,236 Total Exon Count: 10 Strand: -
Coding Region
Position: hg19 chr9:124,967,039-124,991,019 Size: 23,981 Coding Exon Count: 10
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
Primer design for this transcript
Genetic Association Studies of Complex Diseases and Disorders
Genetic Association Database (archive): LHX6
CDC HuGE Published Literature: LHX6
MalaCards Disease Associations
Comparative Toxicogenomics Database (CTD)
Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
Protein Domain and Structure Information
Pfam Domains: PF00046 - Homeobox domain
PF00412 - LIM domain
PF05920 - Homeobox KN domain
SCOP Domains: 46689 - Homeodomain-like
57716 - Glucocorticoid receptor-like (DNA-binding domain)
ModBase Predicted Comparative 3D Structure on Q9UPM6-3
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.
Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Mouse Rat Zebrafish D. melanogaster C. elegans S. cerevisiae
No ortholog No ortholog No ortholog No ortholog No ortholog No ortholog
Gene Details
Gene Sorter
Descriptions from all associated GenBank mRNAs
AL136570 - Homo sapiens mRNA; cDNA DKFZp761G2023 (from clone DKFZp761G2023).LF205667 - JP 2014500723-A/13170: Polycomb-Associated Non-Coding RNAs.AK126982 - Homo sapiens cDNA FLJ45036 fis, clone BRAWH3019629, highly similar to LIM/homeobox protein Lhx6.1.JD250239 - Sequence 231263 from Patent EP1572962.JD516578 - Sequence 497602 from Patent EP1572962.JD459225 - Sequence 440249 from Patent EP1572962.JD195479 - Sequence 176503 from Patent EP1572962.BC103936 - Homo sapiens LIM homeobox 6, mRNA (cDNA clone MGC:119542 IMAGE:40008208), complete cds.BC103937 - Homo sapiens LIM homeobox 6, mRNA (cDNA clone MGC:119544 IMAGE:40008210), complete cds.BC103938 - Homo sapiens LIM homeobox 6, mRNA (cDNA clone MGC:119545 IMAGE:40008211), complete cds.JD114542 - Sequence 95566 from Patent EP1572962.JD216473 - Sequence 197497 from Patent EP1572962.JD514503 - Sequence 495527 from Patent EP1572962.JD102509 - Sequence 83533 from Patent EP1572962.JD250800 - Sequence 231824 from Patent EP1572962.JD306960 - Sequence 287984 from Patent EP1572962.JD448551 - Sequence 429575 from Patent EP1572962.JD484256 - Sequence 465280 from Patent EP1572962.JD163298 - Sequence 144322 from Patent EP1572962.JD153875 - Sequence 134899 from Patent EP1572962.JD200580 - Sequence 181604 from Patent EP1572962.JD390808 - Sequence 371832 from Patent EP1572962.JD349346 - Sequence 330370 from Patent EP1572962.JD165468 - Sequence 146492 from Patent EP1572962.JD215119 - Sequence 196143 from Patent EP1572962.JD331374 - Sequence 312398 from Patent EP1572962.JD086691 - Sequence 67715 from Patent EP1572962.JD308425 - Sequence 289449 from Patent EP1572962.JD237236 - Sequence 218260 from Patent EP1572962.JD217726 - Sequence 198750 from Patent EP1572962.LF347003 - JP 2014500723-A/154506: Polycomb-Associated Non-Coding RNAs.JD474839 - Sequence 455863 from Patent EP1572962.JD503957 - Sequence 484981 from Patent EP1572962.JD169082 - Sequence 150106 from Patent EP1572962.AK299709 - Homo sapiens cDNA FLJ55589 complete cds, highly similar to LIM/homeobox protein Lhx6.1.AK297175 - Homo sapiens cDNA FLJ55755 complete cds, highly similar to LIM/homeobox protein Lhx6.1.LF347004 - JP 2014500723-A/154507: Polycomb-Associated Non-Coding RNAs.JD222462 - Sequence 203486 from Patent EP1572962.AK289827 - Homo sapiens cDNA FLJ77966 complete cds, highly similar to Homo sapiens LIM homeobox 6 (LHX6), transcript variant 1, mRNA.JD254108 - Sequence 235132 from Patent EP1572962.JD061767 - Sequence 42791 from Patent EP1572962.JD226833 - Sequence 207857 from Patent EP1572962.JD054669 - Sequence 35693 from Patent EP1572962.JD321901 - Sequence 302925 from Patent EP1572962.JD455268 - Sequence 436292 from Patent EP1572962.JD098413 - Sequence 79437 from Patent EP1572962.AB031041 - Homo sapiens hLhx6.1a mRNA for LIM-homeodomain (LHX) protein 6.1a, complete cds.AB031042 - Homo sapiens hLhx6.1b mRNA for LIM-homeodomain (LHX) protein 6.1b, complete cds.AK313808 - Homo sapiens cDNA, FLJ94426, Homo sapiens LIM homeobox 6 (LHX6), mRNA.KJ902431 - Synthetic construct Homo sapiens clone ccsbBroadEn_11825 LHX6 gene, encodes complete protein.EU446700 - Synthetic construct Homo sapiens clone IMAGE:100070068; IMAGE:100011909; FLH257163.01L LIM homeobox 6 (LHX6) gene, encodes complete protein.AM392697 - Synthetic construct Homo sapiens clone IMAGE:100001678 for hypothetical protein (LHX6 gene).AM393362 - Synthetic construct Homo sapiens clone IMAGE:100001731 for hypothetical protein (LHX6 gene).LF211803 - JP 2014500723-A/19306: Polycomb-Associated Non-Coding RNAs.LF212883 - JP 2014500723-A/20386: Polycomb-Associated Non-Coding RNAs.MA582580 - JP 2018138019-A/154506: Polycomb-Associated Non-Coding RNAs.MA582581 - JP 2018138019-A/154507: Polycomb-Associated Non-Coding RNAs.MA441244 - JP 2018138019-A/13170: Polycomb-Associated Non-Coding RNAs.MA447380 - JP 2018138019-A/19306: Polycomb-Associated Non-Coding RNAs.MA448460 - JP 2018138019-A/20386: Polycomb-Associated Non-Coding RNAs.
Other Names for This Gene
Alternate Gene Symbols: LHX6.1, NM_014368, NP_055183, Q9UPM6-3UCSC ID: uc004blx.4RefSeq Accession: NM_014368
Protein: Q9UPM6-3 , splice isoform of Q9UPM6
CCDS: CCDS6838.2
Gene Model Information
category:
coding
nonsense-mediated-decay:
no
RNA accession:
NM_014368.4
exon count:
10 CDS single in 3' UTR:
no
RNA size:
3444
ORF size:
1179 CDS single in intron:
no
Alignment % ID:
100.00
txCdsPredict score:
2458.00 frame shift in genome:
no
% Coverage:
99.71
has start codon:
yes
stop codon in genome:
no
# of Alignments:
1
has end codon:
yes
retained intron:
no
# AT/AC introns
0
selenocysteine:
no
end bleed into intron:
0 # strange splices:
0
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Methods, Credits, and Use Restrictions
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