AMCG00005544 (lhx1a,LOC105897175,LOC105023804,LOC106613102,LOC106581220,LOC107685180)


Basic Information

Item Value
gene id AMCG00005544
gene name lhx1a,LOC105897175,LOC105023804,LOC106613102,LOC106581220,LOC107685180
gene type coding
species bowfin (Amia calva)
category of species ecological fish

Chromosome Information

Item Value
chromosome id CM030142.1
NCBI id CM030142.1
chromosome length 21087710
location 4479446 ~ 4490819 (+)
genome version AmiCal1_2021_bowfin_Genome

Sequence

>AMCG00005544
ATGGTCCACTGTGCTGGGTGCGAGAGGCCTATACTGGACAGGTTTCTGCTCAACGTGCTGGACAGGGCTTGGCATGTGAAGTGCGTTCAGTGCTGCGAGtgtaaatgcaatttaacaGAGAAATGCTTTTCTCGGGAAGGGAAACTCTACTGCAAAAACGACTTCTTTAGGCGCTTTGGTACCAAGTGCGCGGGCTGTTCGCAGGGCATCTCGCCCAGTGACCTGGTGCGGAGGGCCAGGAGCAAAGTCTTTCACTTGAACTGTTTCACCTGCATGATGTGCAACAAGCAGCTCTCCACTGGGGAGGAACTCTACATCATAGACGAAAACAAATTTGTCTGCAAAGAAGATTACTTAAGCAACAGCAATAACACGAAAGACACAAACCTTCTCTCAGTGACGGCGTGCAGCGACCCCAGCTTATCCCCGGACTCTCAAGACCAGTTACAGGACGACGTGAAGGACTTGGAAAGTGCGAATCTGTCGGACAAGGAAACGGGTAACAATGAAAACGACGACCAGAACCTGGGCGGCAAGCGGCGCGGGCCGAGGACCACCATCAAGGCCAAGCAGCTGGAGACCCTGAAGGCGGCGTTCGCGGCGACCCCCAAACCCACCCGACACATCCGGGAGCAGCTGGCCCAGGAGACGGGCCTCAACATGCGCGTCATTCAGGTGTGGTTCCAGAACCGGCGCTCCAAAGAGCGGCGCATGAAGCAGCTGAGCGCCCTGGGGGCCCGACGGCACGCCTTCTTCCGCAGCCCCCGCAGGATGCGCACCCTGGTGGACCGCCTGGAGCCCGGAGAGCTCATCCCCAACGGCCCCTTCTCCTACTACGGAgATTATCAAAGCGAGTATTACGGCCCCGGAAGCAACTACGATTTCTTCCCCCAGGGGCCCCCATCCTCACAGGCCCAGACCCCAGTGGACCTGCCTTTCGTCCCGTCCTCGGGCCCCACCGGCACCCCGCTGGGGGGCATGGACCACCCCCTGCCCGGCCACCACCCGTCCAGCGAGGTGCAGCGTTTCTCGGACATCCTGTCTCACCACCCCGGGGACTCGCCCAGCCCGGAGCCGGGCATCCCGGGACCTCTGCACAGCATCTCCTCAGAAGTGTTCGGCCCGAGCCCACCCTTTACCTCACTCTCCATCAACGGCAGCGGCTACAGCAACCACCTCTCACATCCCCCGGCCGAAATGAACGAAGCCACTGTTTGGTAG

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).

NR:

description
LIM/homeobox protein Lhx1

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:0006366 transcription by RNA polymerase II biological_process
GO:2000744 positive regulation of anterior head development biological_process
GO:0009880 embryonic pattern specification 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: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:0009791 post-embryonic development biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0003714 transcription corepressor activity molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG:

id description
K09372 LHX1; LIM homeobox protein 1

RNA

RNA id representative length rna type GC content exon number start site end site
AMCG00005544 True 1221 mRNA 0.60 5 4479446 4490819

Neighbor

gene id symbol gene type direction distance location
AMCG00005537 NA coding upstream 169298 4305625 ~ 4310148 (+)
AMCG00005534 phf12 coding upstream 199001 4264415 ~ 4280445 (+)
AMCG00005536 NA coding upstream 228598 4240208 ~ 4250848 (+)
AMCG00005535 LOC107690431,LOC107592631,LOC107743685 coding upstream 251756 4219881 ~ 4227690 (+)
AMCG00005567 LOC107718289,LOC105897181 coding upstream 486167 3918356 ~ 3993279 (+)
AMCG00005545 LOC103910010 coding downstream 4789 4495608 ~ 4520105 (+)
AMCG00005553 NA coding downstream 114057 4604876 ~ 4615951 (+)
AMCG00005554 NA coding downstream 135294 4626113 ~ 4635255 (+)
AMCG00005577 appbp2 coding downstream 493411 4984230 ~ 5000598 (+)
AMCG00005580 usp32,LOC107585566,LOC108425843 coding downstream 531452 5022271 ~ 5067746 (+)
G152906 NA non-coding upstream 186564 4292030 ~ 4292882 (+)
G152866 NA non-coding upstream 218811 4258866 ~ 4260635 (+)
G152764 NA non-coding upstream 717619 3723913 ~ 3761827 (+)
G152657 NA non-coding upstream 1219017 3260210 ~ 3260429 (+)
G152656 NA non-coding upstream 1279259 3199332 ~ 3200187 (+)
G152943 NA non-coding downstream 41502 4532321 ~ 4534824 (+)
G153080 NA non-coding downstream 699708 5190527 ~ 5190796 (+)
G153082 NA non-coding downstream 704969 5195788 ~ 5201535 (+)
G153113 NA non-coding downstream 817126 5307945 ~ 5309091 (+)
G153118 LOC106602865,LOC108260233,LOC108429749,LOC105010822,LOC103035912,LOC105896079 non-coding downstream 830241 5321060 ~ 5323923 (+)
AMCG00005538 NA other upstream 174290 4282517 ~ 4305156 (+)
AMCG00005498 lyrm9,LOC102789908 other upstream 1208602 3266374 ~ 3270844 (+)
G152588 rpl23a other upstream 1629838 2845217 ~ 2849608 (+)
AMCG00005481 dynll2a,LOC107554284,LOC103397138 other upstream 1968770 2503910 ~ 2510676 (+)
AMCG00005429 ywhae,LOC106567579,LOC105005922 other upstream 2532646 1929455 ~ 1946800 (+)
AMCG00005546 acaca,LOC107691719 other downstream 69394 4560213 ~ 4563020 (+)
AMCG00005583 LOC106603777,LOC105895333,LOC108428505 other downstream 723994 5214813 ~ 5241776 (+)
AMCG00005647 NA other downstream 1943702 6434521 ~ 6437078 (+)
AMCG00005667 NA other downstream 1996899 6487718 ~ 6488782 (+)
AMCG00005663 NA other downstream 2117824 6608643 ~ 6662480 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000072_00629638_00638277 LHX1, LHX1A, LHX1.L coding CI01000072 null 629638 ~ 639351 (+)