XLOC_017454 (lmx1a)


Basic Information

Item Value
gene id XLOC_017454
gene name lmx1a
gene type coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007131.7
NCBI id CM002904.2
chromosome length 55201332
location 33922339 ~ 33940260 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00034686
ATGACTCTCTGGATAATGATGTGCCAGATGGATGACACGTTTGTCGTTTTTGCAGACATGTGGAGAAAGAGCGTGTGTGAGGGGTGTAATGAGCTCATCCGGGACAGGTACCTGCTCCGCGTGCAGGACGGGCTGTGGCACGAGCGCTGCCTGCACTGCGCATCATGTCGCGAGCCTCTGAAAGACACCTGCTTTCTCCGCAATAAAACACTCTACTGCAAGCGAGACTACCAGAAGCTGTTTGTGGTGCGGTGTCAGGGCTGCTCAGAGATCATCTCTCCGTCTGAGCTGGTGATGCGCGCACAGGGCTCTGCTGTTTTTCACCTGCGCTGCTTCTGCTGCTGTGTGTGCGGCTGCCGGCTGCAGAAGGGAGATCACTGTGTGCTCCGAGGAGACGGCCTCTTCTGTGCCACACACTTCCACAACCAACTGGCCAGTCCCACCTCCTCTGACTCAGGTAAAAGTGAGGATATTGAGGAGGACAACGATGATGAAGACAACTTGAAGACTGCAGGAGAGTCAAACATAACAGGAGACGTGGAACACAAGAGGCCTAAAAGACCTCGTACCATCCTGACAACACAACAGAGACGGGCTTTCAAAGCTTCTTTTGAGGTTTCATCCAAACCCTGCCGAAAGGTGAGGGAGACTCTGGCAGCAGAGACAGGACTGAGCGTACGAGTCGTTCAGGTCTGGTTCCAGAACCAAAGAGCCAAGATGAAAAAACTGGTGAGAAGACAACAGCAGCAGAAGCAAACTGTGTGCCCACAGGAGAAGAGGGAGAGTCCATCACAACAACATACTGCGACCTCTTGTGGAGCTCTGCCTGTTGAGCTGGAATGTGCAGGTTCATATCCACTTCCCCAGCAGAATCTCAGTCTAGACTCACAGAGCTTGAAGCTGGACCCCTTCAGACAGGGCCTGACCCCTCCTCAGATGCCCGGAGACCACATGCATCCCTATgGTTGTGATACACTCTATGATGAAACAGACAGTGACCCTCTGTGTCATTTTGGAGACTGTATGTCGTCCAGTGAACTTTCCTTTTTAACACCCATTGACCGATTGTATTCAATGCAAGATTCGTATTTCGCCTCTTGAGCATCATTCTGACGGCTCATTAAAGATTTATGaaggagcgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgggtgaatgtATACGCGTGCTTGTATATGTTCTGCTTATGCATGTTTTAGTGTAGAAATGGTTGTGATTGGCGACAAAGGAAATGTACCgtgataaatattatttgtttaatttgtatttattatttttatgtgtgtaATCTTGACTGAATTACAATAAAATGCTCATGACG
>TCONS_00034687
CATCGACACGATGCTCGGACCCCCTCGGCTACCCCAAAACTCAGTCTGATTCACATTCTCACCTCCAAATGCGAAAAAGTCTGCCAAACGACCGAGCGTGATCGACGTTAGTAAAGGTAAAGGCTGTTTGTGGTGCGGTGTCAGGGCTGCTCAGAGATCATCTCTCCGTCTGAGCTGGTGATGCGCGCACAGGGCTCTGCTGTTTTTCACCTGCGCTGCTTCTGCTGCTGTGTGTGCGGCTGCCGGCTGCAGAAGGGAGATCACTGTGTGCTCCGAGGAGACGGCCTCTTCTGTGCCACACACTTCCACAACCAACTGGCCAGTCCCACCTCCTCTGACTCAGGTAAAAGTGAGGATATTGAGGAGGACAACGATGATGAAGACAACTTGAAGACTGCAGGAGAGTCAAACATAACAGGAGACGTGGAACACAAGAGGCCTAAAAGACCTCGTACCATCCTGACAACACAACAGAGACGGGCTTTCAAAGCTTCTTTTGAGGTTTCATCCAAACCCTGCCGAAAGGTGAGGGAG
>TCONS_00034688
ATCGACACGATGCTCGGACCCCCTCGGCTACCCCAAAACTCAGTCTGATTCACATTCTCACCTCCAAATGCGAAAAAGTCTGCCAAACGACCGAGCGTGATCGACGTTAGTAAAGGCTGTTTGTGGTGCGGTGTCAGGGCTGCTCAGAGATCATCTCTCCGTCTGAGCTGGTGATGCGCGCACAGGGCTCTGCTGTTTTTCACCTGCGCTGCTTCTGCTGCTGTGTGTGCGGCTGCCGGCTGCAGAAGGGAGATCACTGTGTGCTCCGAGGAGACGGCCTCTTCTGTGCCACACACTTCCACAACCAACTGGCCAGTCCCACCTCCTCTGACTCAGGTAAAAGTGAGGATATTGAGGAGGACAACGATGATGAAGACAACTTGAAGACTGCAGGAGAGTCAAACATAACAGGAGACGTGGAACACAAGAGGCCTAAAAGACCTCGTACCATCCTGACAACACAACAGAGACGGGCTTTCAAAGCTTCTTTTGAGGTTTCATCCAAACCCTGCCGAAAGGTGAGGGAGACTCTGGCAGCAGAGACAGGACTGAGCGTACGAGTCGTTCAGGTCTGGTTCCAGAACCAAAGAGCCAAGATGAAAAAACTGGTGAGAA

Function

symbol description
lmx1a 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 neuron differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in brain; cranial ganglion; and otic vesicle. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 7. Orthologous to human LMX1A (LIM homeobox transcription factor 1 alpha).

GO:

id name namespace
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: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-041014-332 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 neuron differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in brain; cranial ganglion; and otic vesicle. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 7. Orthologous to human LMX1A (LIM homeobox transcription factor 1 alpha).

Ensembl:

ensembl_id ENSDARG00000020354

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00034686 False 1374 mRNA 0.49 7 33922339 33940260
TCONS_00034687 False 534 mRNA 0.53 4 33924235 33936662
TCONS_00034688 True 615 mRNA 0.53 5 33924236 33938675

Neighbor

gene id symbol gene type direction distance location
XLOC_017453 rxrgb coding upstream 2284 33875256 ~ 33920055 (+)
XLOC_017452 olfml2ba coding upstream 115831 33792156 ~ 33806508 (+)
XLOC_017451 henmt1 coding upstream 173165 33744065 ~ 33749174 (+)
XLOC_017450 ppil6 coding upstream 179044 33739059 ~ 33743295 (+)
XLOC_017449 ak9 coding upstream 184508 33708318 ~ 33737831 (+)
XLOC_017455 BX296562.2 coding downstream 19310 33959570 ~ 33975292 (+)
XLOC_017456 si:dkey-51e6.1 coding downstream 41686 33981946 ~ 33985743 (+)
XLOC_017457 zp3a.2 coding downstream 47205 33987465 ~ 33989427 (+)
XLOC_017458 zp3a.1 coding downstream 51541 33991801 ~ 33993698 (+)
XLOC_017459 si:dkey-97o5.1 coding downstream 54320 33994580 ~ 34010235 (+)
XLOC_017441 NA non-coding upstream 863795 33057784 ~ 33058544 (+)
XLOC_017440 NA non-coding upstream 1072236 32827420 ~ 32850103 (+)
XLOC_017433 CU138515.1 non-coding upstream 1451885 32466886 ~ 32470454 (+)
XLOC_017431 BX927123.1 non-coding upstream 1519979 32270907 ~ 32402360 (+)
XLOC_017430 BX842669.1 non-coding upstream 1681370 32231609 ~ 32240969 (+)
XLOC_017471 BX279523.2 non-coding downstream 721295 34661555 ~ 34663198 (+)
XLOC_017472 BX279523.3 non-coding downstream 723062 34663322 ~ 34664762 (+)
XLOC_017475 NA non-coding downstream 821483 34761743 ~ 34766443 (+)
XLOC_017476 NA non-coding downstream 824190 34764450 ~ 34765817 (+)

Expression


Co-expression Network