XLOC_021146 (lhx9)


Basic Information

Item Value
gene id XLOC_021146
gene name lhx9
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007133.7
NCBI id CM002906.2
chromosome length 39133080
location 23238790 ~ 23253481 (-)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00041519
ATCCACTCGGATGTTTTAAGGATCCGGAAAGCTGTATATGGAAGTTGTGGGGTGCAAGGCGAAAGAAAGCAGTTGCACATTGCGTCCAGCAGCCATGCTTTTCCACGGCATCTCTGGGGATCATATTCAAGGGATCATGGAGGAGATGGAGAGGAGATCTAAATCGGAGTCTCGACTAGCAAAAACCGTCCAGATGAACGGACGGGAGACGactatgCCCTCCATGAGCCCAGAGAAGCCTGCGCTGTGCGCCGGCTGCGGTGGTAAAATCTCCGACAGATACTACTTACTCGCCGTTGATAAACAGTGGCATTTAAGGTGTCTCAAGTGTTGTGAATGTAAACTGGCCCTTGAATCCGAACTGACGTGTTTCGCAAAGGATGGCAGCATTTACTGCAAAGAGGATTACTACAGAAGGTTCTCCGTGCAGAGATGTGCCCGCTGCCACCTCGGCATATCCGCTTCGGAAATGGTGATGCGCGCCAGGGACTCCGTGTACCATCTGAGCTgcttcacctgcaccacatgcaACAAAACACTGACCACGGGTGACCATTTCGGCATGAAAGACAACTTGGTTTACTGCCGGGTTCACTTTGAGACCCTTATTCAGGGAGAGTATCACCCTCAATTAAACTACGCTGAATTAGCGGCCAAAGGCGGAGGGCTTGCGCTGCCTTACTTCAATGGCACCGGCACGGTGCAGAAAGGAAGGCCACGAAAGAGGAAGAGTCCGGCGATGGGGATTGACATCGGCTCTTACAGCTCAGGTTGTAATGAGAACGATGCGGACCATTTGGATCGGGATCAGCAACCCTACCCTCCTTCCCAGAAGACCAAGCGCATGCGTACATCATTCAAACACCATCAGCTTCGCACCATGAAGTCCTACTTTGCCATTAACCACAACCCCGATGCCAAGGACTTAAAACAACTCGCCCAAAAGACAGGACTGACCAAGAGAGTTCTTCAGggAGAACAAATCTTGGGGCATTACAGCCATACTTCACGACGTTTGAAAATTCCCTAAAGTATTAAAAGAAGCTTTGATCGGAATTCTTCACCATTGAAGACAAAGACAGTATTAGGATCAGATTTTAGTCATTTCAAATctaccaaaaaagaaaatgatgttTTCCAAAATCTTTTTGTTTTTCCTCTTTAAAAAACATCCTGAATGATTAAAAGCCTTCTTCTACAACAAATGGGATATTTTTTGTGACTGTAATGAGGCCAAAAGGCAAACTAAGCTGTACAGTATTGTAGATACGTAACAGAGCAACCTTGCTCCAAGAGGCGACTGCAGGAGACGGATCTACGCACGCATGcatgtctacacacacacatatacacaaactaCCTTGTAATTCTGCTTGCTGTAAAACATTCCTGTGCAACAAATGTCACTTATCATGAACGCACAGCCTTCCTAAAACTTGGCAGGAAAATGTCCGACCAGGAGAAGCTGGAAAGGAACACCATATGgctgtatttaaaatacaagttataagagagaaagaaaaaaaagaagagaaaattCTGCATGCACTTCTCATTGTTGACGGCTATTTCAGATGGATATTATTTCATATTGATGTTTCATTTGTTGTCTGTTGTGTACTTAAAGGAGTTTTCTTGTAAATTCAAACCTTACCGACAAAATCGACAGTTTAAATACGTAAACGCATGCTTGATTTGACAACAAAAACTGTTTATCTTAGGAAAAAACATTTGGGTTTACTGCTTTTCATAGTAATACATTCTTGTGGTgttagtttaaaaacaaatatgaatgaataaataaaataaagaagggAAATGATCAGATTTCACTGTcggtgttttaaaatgttttgttgaatTGTAACTATCCTGAAATAAAGATTGTGTAAAGTCTGAGGGGAAAGAAAGGCCACATGGGGGCCTAGTAAACACTGAAGTGTTGAATTCCTGCTATGCCAGACGTGTCAATGAAGCTTTGCGCCGGATGACCACAAAACCTAATTCTTTTCAGTCTGTGGGCAATttcttcataaaaaaaataaaaagcttagtCGGGCAGACTAAAATGCGCTTTAAACACTGAATCTGACTGATTTCAACAGTCAAATTAGGTAGAAATGCACACTGTACTACTATAAAATCTAAAATGTGAAAGTAAATAAAGCTGGGTTTAAGTCATCAGGCTGGGAAAGGAGACCTTGAGATCAAAAAGAGGATTTTTTTTACACACTCGGAGGAGTGGAATGGTCAGCGTAACCAGAAGCTAACAGGAAGACTGATGCTGTCCTCCcttcagaaaacaaaacacaaggaGACACACTGCATGAGGAATCAGGAAGGTTTGTGAGAATTGTGTTTACATGTGCATGCTCTCGGTTTATgtcacaaaaacgtaaaaaaaaaataataataaaaaaagcaacaaatttaaaataattaagctattaaaaggatggttcactcaaaactgaagaGAATGCTGTCTTTGCGAATTCATCCTCATGTTGTTATTAAGTTCTTCTATCACAGTTGTCTTCTAATAAATGGTTGCACATCATAACATCTCAAACCATGTTTAGCTTCATTTAAGTCTGCAATTAAAAgtcattaattttaatatttattaaattatttcatgCTAATGTTGGATAATAATGCTGCTAAAActtgtaaaaaaatacacaagGATATTTCAGTGTCTGGGATGGAATTCAATTCACAAAATTGCTTTGTATGAGGAGAATGTACAGTTGAATAAacagtggctaataattcagggggcctaataattctgacttcaattgtgtgtgtatgtatatgtgtgtatttgtatacacacacacacacacacacacacacacacacatatatatagttgaagtatatatagttgaagtcagaattattagcctccctttgaattgtATTTTCTTCTTTAACAGATCAAGGGAAtattcacaatatgtctgataatattttttcttcttaagaaagtcttatttgttttattttgaatagaaTATAAGTAGTTTTCAGTTTGTTtgaaaccattttagggtcaaaattattagcccctttaagctatttattttttccgatagtctacagaacaaaccatcgctatacataaacttgtctaattacccaaacctgcctagttaacctaaataacctagttaaacctttaattgtaactttaagctgtatagaagtgtcttaaaaatatcttgtcaaatactatgtaaatattacatgtaaataattattatgctgtcatcatggcaaagataaaataaatcaattagaaaagagttattaaaactattatgtttagaaatgtgctgaaaaaatgttctctccattaaacagaaattggggaaaaaaattaacaaggggtttaataattcagggggcctaataattctgacatataTTCTGACATAAAttctgacatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatagtgtgaactaaattaaatgttttgatggTCTTAATTGCATGTCGTTTACGATTAAGTGAAAAAGTAATACAGTTTAAATTGAAGTTAAAGTGTACTGCTGGATGTATTACAAACATTTGTGGTAACTAAAGTACACTTTAATGTTACTTCTGAtgaggtatttaaaaaaaagttcaatttagtatagtttaaaataaataaatggtacaAATGTATTCATCTGATTGTTCTATAGTACATCAATCAACATAAATATATGTGTACATATTGTGTAATATATTGTATGTGTTACTTTAACGATTGACACAAGTATAAAACAAtgcactgtttacattttaaattttttcattcattcattttccttcaccttAGTCCCCTATTTATCTATTCTAGCATATTAgcactattccagcatatgttttacattgatggtgcccttccagtcgcaaaccagtactgggaaacacccatacacactctcatttacacacacacatacactacagctaatttagcacatgtctttggaccgagGGGAAACTGAAGCAGCCGGTGGAAACCTACGTGaatacgggaagaacatgcaaactccacacagaaatgccaactggcccaagtGCGAgtcgatcttcttgctgtgaggtgacagtgctaaccactgagccaccgtgcctttttacacttttttttacctTATTACAAAGTGTATTTCTCAAAACTATGCGTTAAAATCATGTACAGCAATATAAGATGAGTTTCTCTGGATTCActagatttaaaatattattatttgctttattctataaaggtctgaTACATATTTGAATTTCCGatcaaaataatatgtttttttattttgttgcagaaaatgacaattaatcagaataacaaatgttttcatttgctgTTGTTgaaaaatcagggttattccagcAATTATTAATTtcaaagttatttattattttgaacaatTATACAATATAACGAAAACAataacattattgttattttgcgCAATTGTCATTTTATGCTCTAAATGACAGTAAGCAAATTttgaagaaatgtcatcagtaatttacagtataaaacaaaaatgatgttttactcatgtttcccagtattgggttgcagctggaaggtcatccacagcttaaaacatatgctggaatagatggcggttcattccactgtggcgacctctaaaataaagactaggccaaaataaaattaatgcattttttactcaaacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacacttgtacatgtATATTTATGGGGACTTCCTATAGATGTAATGTTTCTTATATGGTACAAATTGTACATTCTTTCCTTCCAACCTAACCCTACTCCAAAACCCAATcctcacaagaaaaaaaatcagattttttttttttcattttcaaaatatttaatttccttgtggagacaaaaaaaaaatccccacaaagtattatttatttgacGTGAGGAATACAAAGTACACTACTTAACACACTATTTTAAAGTGCTCTAGTTACCGTGCAACTATTCATTTAATTGCTGAGTAATATCAATTAATGGCATGTACATTGCATTACTATATGGTTAGTTATATAACTATATAGTAAGTACATGGAACttgtaacaaggacaccttaaaataaggcgttacctgttttttttatttttttatggtatTCAGATTACATGtacatctttattaaagttatacTCTTTTACATGTAAACCATTGCACACTTCTCCCCCGGTCTGTTAACTTATCAGGCTATATACAGCTTGTAGGCCATTAAGGTCCCAGAtcagtttgttttgtctgtcCCTCTGtctcgctgcaaatcaaaaggtgatcgTGTTTCTGTTTTGCAGCCTGCAACAGTCTCCCTTTGAATATTATGATTTCTCCATCATTTGATGCCTTTAAATGTAAAcctaaagacttatttttactccCTTGCCTTTGAGTGGTACATGCATGCtatttcttatctgtattttagtattacatatatatatttcctttttctcatattttaatacaagttatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatataaatttattttata
>TCONS_00041520
CTTTCACGCATTCGGATCCTCAGTTGGAGATTGGGACTATCTGAAAACCCACGTTTAAAACATCCTCCAGACTTCAGTTTTGCCTTATATCATCCGGACTATACTTTTTTCTGACGTTGGAGAAAGTGGACTGGTTCTCCTGACTGTTCCTGCGCCGTCCATCAAATTCCACCGgcttaatatttttgtaacaCATTGATTGCATTTTGTTGTGAATCTGTTGGTGTAGATCCACTCGGATGTTTTAAGGATCCGGAAAGCTGTATATGGAAGTTGTGGGGTGCAAGGCGAAAGAAAGCAGTTGCACATTGCGTCCAGCAGCCATGCTTTTCCACGGCATCTCTGGGGATCATATTCAAGGGATCATGGAGGAGATGGAGAGGAGATCTAAATCGGAGTCTCGACTAGCAAAAACCGTCCAGATGAACGGACGGGAGACGactatgCCCTCCATGAGCCCAGAGAAGCCTGCGCTGTGCGCCGGCTGCGGTGGTAAAATCTCCGACAGATACTACTTACTCGCCGTTGATAAACAGTGGCATTTAAGGTGTCTCAAGTGTTGTGAATGTAAACTGGCCCTTGAATCCGAACTGACGTGTTTCGCAAAGGATGGCAGCATTTACTGCAAAGAGGATTACTACAGAAGGTTCTCCGTGCAGAGATGTGCCCGCTGCCACCTCGGCATATCCGCTTCGGAAATGGTGATGCGCGCCAGGGACTCCGTGTACCATCTGAGCTgcttcacctgcaccacatgcaACAAAACACTGACCACGGGTGACCATTTCGGCATGAAAGACAACTTGGTTTACTGCCGGGTTCACTTTGAGACCCTTATTCAGGGAGAGTATCACCCTCAATTAAACTACGCTGAATTAGCGGCCAAAGGCGGAGGGCTTGCGCTGCCTTACTTCAATGGCACCGGCACGGTGCAGAAAGGAAGGCCACGAAAGAGGAAGAGTCCGGCGATGGGGATTGACATCGGCTCTTACAGCTCAGGTTGTAATGAGAACGATGCGGACCATTTGGATCGGGATCAGCAACCCTACCCTCCTTCCCAGAAGACCAAGCGCATGCGTACATCATTCAAACACCATCAGCTTCGCACCATGAAGTCCTACTTTGCCATTAACCACAACCCCGATGCCAAGGACTTAAAACAACTCGCCCAAAAGACAGGACTGACCAAGAGAGTTCTTCAGGTTTGGTTCCAAAATGCACGGGCCAAATTCAGAAGAAACGTTTTGCGGCAGGAGAATGGGGGTGTTGATAAGGCTGACGGCACGTCACTTCCGCCACCCTCTTCCGACAGCGGTGCTCTGACCCCACCAAGCACGGCCACCACACTAACTGACCTGACCAATCCCTCTATCACCGTAGTAACTTCAGTCACCTCTAGTTTGGACAGCCACGAATCTGGGAGCCCCCCACAAACTACCTTGACAAACCTTTTCTAACACGGAGTTGCTTTTTTTGTCTTTATCCCCCTTTATTTCCagattctatttttattttccacGAAAAAAcgaaaaacagcaacaacacaaAAACCTTTTGGTGACCACCAGAAAGACTTTGGAAATGTAAGACGAGACCTACTAAATGTGTAGCATTTGCAACCGCGTGGCAGCTGAGTTTGTAGTACTTGTc

Function

symbol description
lhx9 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within neuron fate specification and thalamus development. Predicted to be active in nucleus. Is expressed in brain; forebrain neural keel; head; hypocretin-secreting neurons; and testis. Orthologous to human LHX9 (LIM homeobox 9).

GO:

id name namespace
GO:0021794 thalamus development biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0030182 neuron differentiation biological_process
GO:0097380 dorsal spinal cord interneuron anterior axon guidance biological_process
GO:0045892 negative regulation of transcription, DNA-templated biological_process
GO:0048665 neuron fate specification biological_process
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: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-050417-210 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within neuron fate specification and thalamus development. Predicted to be active in nucleus. Is expressed in brain; forebrain neural keel; head; hypocretin-secreting neurons; and testis. Orthologous to human LHX9 (LIM homeobox 9).

Ensembl:

ensembl_id ENSDARG00000056979

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00041519 False 5845 mRNA 0.35 5 23238790 23253252
TCONS_00041520 True 1650 mRNA 0.49 5 23245923 23253481

Neighbor

gene id symbol gene type direction distance location
XLOC_021145 nek7 coding downstream 10121 23105059 ~ 23228669 (-)
XLOC_021144 ptprc coding downstream 170931 22977268 ~ 23067859 (-)
XLOC_021143 BX936380.2 coding downstream 294205 22944461 ~ 22944585 (-)
XLOC_021142 NA coding downstream 377292 22825425 ~ 22861498 (-)
XLOC_021141 NA coding downstream 450062 22770522 ~ 22788728 (-)
XLOC_021147 C22H1orf53 coding upstream 11141 23264622 ~ 23267893 (-)
XLOC_021148 crb1 coding upstream 239689 23493170 ~ 23545828 (-)
XLOC_021149 CR388178.3 coding upstream 243334 23496815 ~ 23496929 (-)
XLOC_021150 f13b coding upstream 331316 23584797 ~ 23591493 (-)
XLOC_021151 NA coding upstream 339576 23593057 ~ 23596961 (-)
XLOC_021139 BX649292.1 non-coding downstream 704327 22533586 ~ 22534463 (-)
XLOC_021137 NA non-coding downstream 715335 22342385 ~ 22523455 (-)
XLOC_021156 BX005398.1 non-coding upstream 499105 23752586 ~ 23754415 (-)
XLOC_021157 BX005398.2 non-coding upstream 504474 23757955 ~ 23758641 (-)
XLOC_021159 AL935303.1 non-coding upstream 715599 23969080 ~ 23969709 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000030_05233712_05242487 LHX9 coding CI01000030 null 5233466 ~ 5242487 (-)
bowfin (Amia calva) AMCG00005157 lhx9,LOC107674936,LOC107556179,LOC107699434,LOC107586419,LOC107741549,LOC107712183 coding CM030140.1 CM030140.1 17522613 ~ 17530487 (-)