XLOC_009279 (lhx1a)


Basic Information

Item Value
gene id XLOC_009279
gene name lhx1a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007126.7
NCBI id CM002899.2
chromosome length 48040578
location 27703409 ~ 27710575 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00018241
GCAGAACTGGTGAATATATTTAAAACTTCTTCATCTTTTCGTTTCAACCCTGTTCGCAAAGACTGACTTGGAACATCCTTCAGCGATACAACTTTTCCTCCTCTCTTTTAAAAGAGAGAAATCAGGAGCAGAGCCTCAGGTTGTGGACACCACGGCAGTAACTGTGGGAGCACATCCAAAGACGATGGTCCACTGTGCGGGCTGCGAGAGGCCTATATTGGACAGGTTTCTCCTTAATGTTCTGGACAGAGCATGGCACATCAAGTGCGTACAGTGCTGCGAGTGCAAATGTAACCTAACAGAGAAATGCTTCTCTCGAGAAGGAAAACTATATTGCAAAAACGACTTCTTTAGGCGCTTTGGAACAAAATGTGCGGGTTGTGCTCAGGGGATCTCGCCGAATGACTTGGTCCGGAGGGCACGGAGCAAAGTGTTTCATCTGAACTGCTTCACATGCATGATGTGTAACAAGCAGCTTTCCACAGGAGAGGAATTGTACATCATAGACGAAAATAAATTTGTCTGTAAAGACGATTATTTAAGCAACACGAACGGAAAAGACTCAAATCTCCTATCAGTTACAGCTTGCAGTGATCCTAGTTTATCGCCAGATTCTCAAGACCAGCTACAGGACGATGTCAAGGATGCGGAAATCGCAAATTTATCGGACAAAGAAACGGGTAACAATGAAAATGATGACCAGAACCTTGGAGGCAAACGGAGAGGACCGCGTACCACTATTAAAGCAAAGCAACTGGAGACACTGAAAGCGGCATTCGCGGCGACCCCCAAACCAACCAGACACATCAGGGAGCAACTGGCGCAAGAGACGGGACTCAACATGCGAGTTATTCAGGTATGGTTTCAGAACCGGCGGTCCAAAGAGCGGCGTATGAAACAGCTGAGCGCGCTCGGCGCCAGGAGACACGCGTTCTTCCGGAGTCCGAGAAGAATGCGAACGCTCGTGGACAGACTCGAGCCTGGAGAATTAATTCCAAACGGCCCGTTTTCATACTATGGAGATTATCAAAGCGAGTACTACGGCCCAGGAGGGAATTACGACTTCTTTCCCCAAGGCCCTCCATCCTCACAGGCCCAGACTCCTGTAGACCTCCCTTTTGTTCCCTCATCAGGACCCACCGGTACCCCACTTGGGGGCATGGACCATCCCATCCCCGGTCACCATCCGTCCAGTGAAGTACAACGCTTTTCAGACATCATGTCTCACCACCCGGGAGACTCGCCTAGTCCTGAACCCGGCATCCCTGGACCCCTGCACAGTATGTCCTCAGATGTTTTCGGGCCCAGTCCGTCCTTTACGTCCCTCTCGCTGAATGGCAGCGGATACAGCAACCACCTCTCCCATCCTCCGTCAGAAATGAACGAGGGCACAGTCTGGTAGCTGCTGTGAATGGACATTCCGTTGGAGGAGGGAGGGTGGGAACGGGGAAACACTGACCGGCCGCACATTCTGGTTctcatttttgtctcttttttcaCCCCCCATGTCATAAATGTGTTTGGAGAGAGCAGTAGAGGGCAGCATGGGCATTGACATTCACCTTCTTGAACTTGTTGTGTTGATGGTCCGTTTTTTTTTCGTTCCTTCTTTGTCCCAAATCCGAACTCAAGAAGAGATACTGTTGACCCGGTCGCTGTATGAACTCCGCTACGAGGCGTCCCTCCACAAATCGGTTTAATCGGCGCTCTAAAAACAGCGATTGCGACACATTAACAGCGTCAGCTACCGTCAAAGACTTGTCAGCTTTACAGAGAAACACCCGAGGCGGCTGATCTAACGCTAACCTGCAATGTTGACTCCAGGAGAGATCTAAGCCGTcagactaatttatttatttgaaaactccTCAGACCTCCTTGCCTTTCAAGGCTCTGCCATACTGACACTTAAACAACCTTTTCGACACTAAATACGTTTCTGAAGGCCAGGGAgaaaagcttttctttttctcgTTCTGGAcatatcctgtttttttttttttttcaattagtttttttctttcccaAGAATTCCACCAAATCTGAAGAAGTTAGCCTTCAAAAGGCGAAACATTCAATGCGTATGGATTGTGCACCCTTTATTTAATGGAAGAGAACTTGAAATGTTGATAAATGAAGTCTACcttctaaaattattttaaccAAGGGTCTGAAAGGGACATAGAACAGTCAACTGTTTACGTAATATATTTAATTCAGGAGTTAAAAAGTATCAACCATGATTTAGAACCTCTTGATTCAGAAAAAAATGTTCCAAGCAACCAACCAAACTTTTGTAtcgattttatttatattgtacgATGAAAATGAGTTTGCTGGGGTTGTGGTTCACTGTGCTAGTTTGTACAAAatgttgtttacaaaaaaaaacttggaaaaaa
>TCONS_00018242
CTACCTCATGAGAAAATCTTCTATCGTCTTCATTTTGGACCCCTACAGGTCCACCCACAAACGCAGAACTGAGAGAAATCAGGAGCAGAGCCTCAGGTTGTGGACACCACGGCAGTAACTGTGGGAGCACATCCAAAGACGATGGTCCACTGTGCGGGCTGCGAGAGGCCTATATTGGACAGGTTTCTCCTTAATGTTCTGGACAGAGCATGGCACATCAAGTGCGTACAGTGCTGCGAGTGCAAATGTAACCTAACAGAGAAATGCTTCTCTCGAGAAGGAAAACTATATTGCAAAAACGACTTCTTTAGGCGCTTTGGAACAAAATGTGCGGGTTGTGCTCAGGGGATCTCGCCGAATGACTTGGTCCGGAGGGCACGGAGCAAAGTGTTTCATCTGAACTGCTTCACATGCATGATGTGTAACAAGCAGC

Function

symbol description
lhx1a Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including animal organ development; gastrulation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Is expressed in several structures, including axis; mesoderm; nervous system; renal system; and shield. Orthologous to human LHX1 (LIM homeobox 1).

GO:

id name namespace
GO:0001705 ectoderm formation biological_process
GO:0001706 endoderm formation biological_process
GO:0021527 spinal cord association neuron differentiation biological_process
GO:0072077 renal vesicle morphogenesis biological_process
GO:0090009 primitive streak formation biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:2000744 positive regulation of anterior head development biological_process
GO:0097379 dorsal spinal cord interneuron posterior axon guidance biological_process
GO:0009880 embryonic pattern specification biological_process
GO:0030182 neuron differentiation biological_process
GO:0007275 multicellular organism development biological_process
GO:0021871 forebrain regionalization biological_process
GO:0061205 paramesonephric duct development biological_process
GO:2000768 positive regulation of nephron tubule epithelial cell differentiation biological_process
GO:0072178 nephric duct morphogenesis biological_process
GO:2000543 positive regulation of gastrulation biological_process
GO:0009953 dorsal/ventral pattern formation biological_process
GO:0021937 cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation biological_process
GO:0045892 negative regulation of transcription, DNA-templated biological_process
GO:0045893 positive regulation of transcription, DNA-templated biological_process
GO:0097477 lateral motor column neuron migration biological_process
GO:0040019 positive regulation of embryonic development biological_process
GO:0021702 cerebellar Purkinje cell differentiation biological_process
GO:0008045 motor neuron axon guidance biological_process
GO:0090190 positive regulation of branching involved in ureteric bud morphogenesis biological_process
GO:0001657 ureteric bud development biological_process
GO:0010842 retina layer formation biological_process
GO:0072049 comma-shaped body morphogenesis biological_process
GO:0072050 S-shaped body morphogenesis biological_process
GO:0060059 embryonic retina morphogenesis in camera-type eye biological_process
GO:0060322 head development biological_process
GO:0009791 post-embryonic development biological_process
GO:0032991 protein-containing complex cellular_component
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function

KEGG: NA

ZFIN:

id description
ZDB-GENE-980526-347 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including animal organ development; gastrulation; and regulation of transcription, DNA-templated. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. Is expressed in several structures, including axis; mesoderm; nervous system; renal system; and shield. Orthologous to human LHX1 (LIM homeobox 1).

Ensembl:

ensembl_id ENSDARG00000014018

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00018241 False 2402 mRNA 0.46 5 27703409 27710513
TCONS_00018242 True 433 mRNA 0.49 3 27708739 27710575

Neighbor

gene id symbol gene type direction distance location
XLOC_009278 NA coding downstream 42292 27660245 ~ 27661117 (-)
XLOC_009275 AL954187.1 coding downstream 44954 27642233 ~ 27658455 (-)
XLOC_009277 AL954187.3 coding downstream 49117 27654176 ~ 27654292 (-)
XLOC_009276 AL954187.2 coding downstream 56873 27646419 ~ 27646536 (-)
XLOC_009274 brip1 coding downstream 180571 27415772 ~ 27522838 (-)
XLOC_009280 NA coding upstream 73975 27784550 ~ 27956162 (-)
XLOC_009281 CR391930.2 coding upstream 212403 27922978 ~ 27923093 (-)
XLOC_009282 CR391930.1 coding upstream 260723 27971298 ~ 27972474 (-)
XLOC_009283 dhrs13a.3 coding upstream 296193 28006768 ~ 28085563 (-)
XLOC_009284 NA coding upstream 300155 28010730 ~ 28015128 (-)
XLOC_009273 NA non-coding downstream 289408 27391544 ~ 27414001 (-)
XLOC_009291 CR478288.1 non-coding upstream 646270 28356845 ~ 28357872 (-)
XLOC_009292 CR478288.2 non-coding upstream 664938 28375513 ~ 28375627 (-)

Expression


Co-expression Network