AMCG00006248 (rxrba,rxrb,LOC107729870,LOC107566635,LOC107751683)


Basic Information

Item Value
gene id AMCG00006248
gene name rxrba,rxrb,LOC107729870,LOC107566635,LOC107751683
gene type coding
species bowfin (Amia calva)
category of species ecological fish

Chromosome Information

Item Value
chromosome id CM030134.1
NCBI id CM030134.1
chromosome length 29342575
location 774474 ~ 785585 (-)
genome version AmiCal1_2021_bowfin_Genome

Sequence

>AMCG00006248
TCAAGACTCCCGCAGTCCAGACAGCTCGTCGGTGTcatccccaccccctcctccagcCCAGCGCTCACCCCCCCTGGCCCCCCCTGCAGCCGCCATgacctccctgcccccccccatgAGCTCAGCGGTCAACTCCCCCATCAGCAGCCTCGGGGGGTCTCCCTTCTCCGTCATCAGCTCTTCGCTGGGCTCCCCCTGCGTCCCAGGGACCCCCTCTGTGGGGTACGGGCCCATCAGCAGCCCACAGatcaaCTCCACGGTGTCCCTGTCAGGGCTGCACGCGGTGAGCAGCTCGGACGACGTGAAGCCGCCTTTCGGCCTGAAGCCCATGTCGGCCCACAGCCCCGGGGGGCCCATGCTGTCCCAGAAACGCCTGTGTGCCATCTGTGGAGACCGCTCCTCCGggaaGCACTACGGGGTGTACAGCTGTGAGGGCTGTAAGGGCTTCTTCAAGCGCACGGTGAGGAAGGACCTGAGCTACACCTGCAGGGACAACAAGGACTGCCTGGTGGACAAGCGGCAGAGGAACCGCTGCCAGTATTGCCGCTACCAGAAGTGTCTTGCCATGGGCATGAAGAGAGAAGTGGTGCAGGATGAACGACAGCGCtCGGTGCAGGAGGAGCGGCAGCGTAACAAGGAGCGCGAGGGGGAGGTGGAGTCCACCAGCGCGGTGAACGAGGAGATGCCGGTTGAGCGCATCCTGGAGGCGGAGCTGGCGGTGGAGCAGAAGACCGAGCTGCACCCGGACGGCCGGGAGACGGGCAGCAACTCGCCCAACGACCCTGTGACCAATATCTGCCAGGCCGCTGACAAGCAGCTGTTCACGCTAGTGGAGTGGGCCAAGAGGATCCCACACTTCTCTGAGCTGCCCCTGGACGACCAGGTCATCCTCCTGCGAGccggcTGGAATGAGCTGCTGATCGCCTCGTTCTCTCATCGCTCCATCTCTGTGAAGGACGGCATCCTGCTGGCTACCGGGCTGCACGTGCACCGGAGCAGCGCCCACAGCGCCGGCGTGGGGGCCATCTTCGACAGGGAGAGTGCGCACAGTGCAGAGGTTGGGGCGATTTTCGACAGggtGCTCACAGAGCTGGTCAGTAAGATGAGAGACATGCAGATGGATAAGACTGAGCTGGGCTGCCTCAGGGCCATCATCCTCTTCAACCCCGATGCGAAGGGTCTGTCCAGCCCCAGCGAGGTGGAGCTGCTGAGGGAGAAGGTCTACGCGTCCCTGGAGGCCTACTGCAAGCAGAGATACCCCGACCAGCAGGGCAGGTTCGCCAAGCTGCTCCTCCGCCTGCCGGCGCTGCGCTCCATTGGTCTGAAGTGTCTGGAGCACCTGTTCTTCTTCAAGCTGATTGGCGACACGCCCATCGACACCTTCCTCATGGAGATGCTGGAGGCTCCACACCAACTCACctagagagaggagagaggaggagagaggggcagggggatgggagacaggagagagagaggagcggagagaggggcagggggtgggagagggaggCAATGGGGTAGTCACAGATGGGGGAGTCTGAAGGAGGGAGTGATTGTGAAGAGGGGAAGCAgtgcacaatacacacacacacacacacacacacacaccctgtctgcatatgaaaagaaaaagtacacaCCCTGAACTTACACAGTTTATACCAGATacagggcccagactggagcagcactGTGGGGGCTGCAGTaaagtatagtgtagtatagggCCCAGAgtggagcagcgctgtgtgaCTGTAGTGTAGTGGCCAGTATTTGTGTACTTGCGTACACTGTATTGGGTCTGAATGCaagtccagtgtgtgtgtacaggcaCAGTGTGATGGGCACTGCTCCAGCCAGGGTGTAAGTGCTGTATATgaggtacagtgtgtgtgtatgttccAGGgccctgtgtgcgtgtgtgtgtcggggTGGTAATGGGGCTGGATGTATTGGGTGCAGGTCCTAACAGAGGCAGtgcagcgggggggggggtgctgtctGGTCCAGCCCTGCCACTGCAGTCTGAGGTCATGTGACTTGACTGTCCATTTTAACAACAAAAGACAGCCTATATGAGGATGCGCCTccaccccctctcctctccgCCTGTCCTCTGATCCAGAGACTTCAGACACAGCtatattttacttcattttgACTCCCACGATTTTAATTACGAAGGCTCTGAAGTGTCGGGAGAAGGACAAATAAAGGAAAGATGGAAgattatgagagagagaggaaagcgAATGTGGGTTTTTCCATGAGGCCAAGGAGGGGAAagaagacaaatatattttataaaaatggaGGAAAACTGAGAGGACGGATTCCCTGCTTCGAGCCCCTGGATCCCGACTGAGGGGCCGCCGGGGCCCGGACTGTCCCCCCACAGCCTCCCACGCCTCTCTCTGGGGCTCCCTGGACCCCACCCGTATTGACTCCCTAAACGAAGCCAGCAAAACAATGGACTCTCCCTGCATTGACTGCCTAAATAACTGTGGATCACTGACTCTCTCCGTGTCCCTCGGAAAATCCTGGATTCCCCCGGAATTCTCAGCGTCTTCTAGAATCTTCTAAcggaattatatatatatatttttttttgttgttgtctgttttgtttgtctctttGATTTTCTTGGCTActgctattactactactagtcCTGTTATTGTCATTATAACTCTTTTCGACTCTCCCGGAGTGAATTTGACTCGTGCCGACTGCTCGGATGTTGTTGGGTTTTTCTGTTCCgtttagtttaatttctgtGCTGCGACGCAGGGGCGCCGGGCTGCCCGTCCTGGAGGCTGCGGGTGTGTCTGTTCCTGTATCTGTCACACTAAGAGTTTAATACAGTTCCCTATGAACCCTCCCGACTCtgctgcctctctgtgtgtgtgcagactcACCAGCGCACTTTGATTCACTCTGACGCAACGTTGCACTGTCCTTTACtatctgacacactgactgatagaTTGGTACAGTCTGACCAACACACTGGCTGATTGATATGTTGATGcactgactaactgacacactggctCACAGACTGAGACGCTTGGCTGACTGATATATTGACGCACTGACCGatagactgacacactggctgatTAAACTCTGGCAGCTCAGGGGTTCTCACTGCACGTCTGGTTTTTGCcagtaaaatactttatttacatCGGTACACACAACGCTCGTAGAC

Function

symbol description
rxrba Contributes to DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in regulation of transcription, DNA-templated. Acts upstream of or within negative regulation of transcription, DNA-templated. Predicted to be located in nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including blastoderm; digestive system; eye; gonad; and tail bud. Orthologous to human RXRB (retinoid X receptor beta).
rxrb Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and nuclear receptor activity. Involved in positive regulation of transcription by RNA polymerase II. Located in nucleoplasm.

NR:

description
PREDICTED: retinoic acid receptor RXR-beta-A-like isoform X2

GO:

id name namespace
GO:0043401 steroid hormone mediated signaling pathway biological_process
GO:0045892 negative regulation of transcription, DNA-templated biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0003707 steroid hormone receptor activity molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:0008270 zinc ion binding molecular_function

KEGG: NA

RNA

RNA id representative length rna type GC content exon number start site end site
AMCG00006248 True 3218 mRNA 0.56 11 774474 785585

Neighbor

gene id symbol gene type direction distance location
AMCG00006244 NA coding downstream 54081 711832 ~ 720393 (-)
AMCG00006239 NA coding downstream 87915 676584 ~ 686559 (-)
AMCG00006242 NA coding downstream 98714 665586 ~ 675760 (-)
AMCG00006240 NA coding downstream 234538 539199 ~ 539936 (-)
AMCG00006238 NA coding downstream 263281 508169 ~ 511193 (-)
AMCG00006255 NA coding upstream 111393 896978 ~ 900845 (-)
AMCG00006259 NA coding upstream 257277 1042862 ~ 1047510 (-)
AMCG00006260 NA coding upstream 262593 1048178 ~ 1049728 (-)
AMCG00006258 psb7,LOC106569939,LOC106588382 coding upstream 282469 1068054 ~ 1073294 (-)
AMCG00006265 NA coding upstream 371142 1156727 ~ 1160200 (-)
G108451 NA non-coding downstream 3137 771111 ~ 771337 (-)
G108427 NA non-coding downstream 61710 585542 ~ 712764 (-)
G108397 NA non-coding downstream 338853 435401 ~ 435621 (-)
G108366 NA non-coding downstream 405850 365278 ~ 368624 (-)
G108365 NA non-coding downstream 496213 270756 ~ 278261 (-)
G108461 NA non-coding upstream 26150 811735 ~ 811963 (-)
G108478 NA non-coding upstream 66699 852284 ~ 855672 (-)
G108480 NA non-coding upstream 72209 857794 ~ 858315 (-)
G108484 NA non-coding upstream 103488 889073 ~ 889802 (-)
G108491 NA non-coding upstream 122305 907890 ~ 909028 (-)
AMCG00006245 LOC106569953,LOC106588396,LOC107101422,LOC107103722 other downstream 25738 726064 ~ 748736 (-)
AMCG00006243 NA other downstream 72534 700535 ~ 701940 (-)
AMCG00006241 NA other downstream 212059 479582 ~ 562415 (-)
AMCG00006232 LOC107694105,LOC107737194,LOC107751684,LOC107575376 other downstream 376575 393832 ~ 397899 (-)
G108379 NA other downstream 431463 333788 ~ 343011 (-)
AMCG00006247 NA other upstream 53270 838855 ~ 874494 (-)
G108708 NA other upstream 340977 1126562 ~ 1134690 (-)
AMCG00006266 NA other upstream 349316 1134901 ~ 1137952 (-)
AMCG00006274 zbtb12,LOC106570057,LOC106588515 other upstream 425701 1211286 ~ 1216184 (-)
AMCG00006277 prrt1,LOC108272790,LOC107694357 other upstream 551602 1337187 ~ 1341665 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000319_05946289_05959917 RXRBA, RXRB coding CI01000319 null 5946289 ~ 5959917 (-)