AMCG00000053 (vps39)


Basic Information

Item Value
gene id AMCG00000053
gene name vps39
gene type coding
species bowfin (Amia calva)
category of species ecological fish

Chromosome Information

Item Value
chromosome id CM030141.1
NCBI id CM030141.1
chromosome length 22147039
location 991040 ~ 1042603 (+)
genome version AmiCal1_2021_bowfin_Genome

Sequence

>AMCG00000053
tggggggaggttgggTGGGATTGTCCTATTGTCCTCTccatagtttttagatttttctgtattgcggtttgttttgttagcatgtttgcttaataacttttcacaaccaaaaaataaatataaatattggtaaaaaaaaatgcagtttagcccctgtataaacttttatatccctaatttatcattggcaccttTTGGCtcttagcaaagtatacaaaccagcactccagccaaaaaaggttcgccatccctggaATAGCCTGCGCTGCAGAGATTGTATCTACTGAGCCACTGATATTgttgtatcatctgcaaatgtgacaagttaGATTAATGGTTGATAGTTTTAAAGcggtacaacaacaacaacaacaacaaaaaactgtggAAACGTTAGAAATGTTTATACAATTTACCTGTAGAAACTTTATATTTGAATGGCATGAATACGTTAACGTATAAATTAAGTAGCATGCATTTCTGTAActtatatatatcatatataaatgcatacgTAAATAATGACGTTTATAGGTGTCGATATTCGCGTTTTGGTTTCTTCTTACTGAAGCAATTTGCGCGGGACAGTAACTGTCTTTCATGGTCAAAATGTCCCCCCGTGAGACAGAGCTGCTGAAATCACGTGTGGAGCAGGACCTGCCTGTGCACTTGAACCAGCAAGAGGAAGTCAAACACAGCGGCGGCGACTTCCGCCATTCATTGCTCAGCGCtagtctatatatatacacgatACATATGTACTATGCATTTAGGAAGTGTATACATCTGTGAATTGCTGTGCAGATTATGTACAAGACATAATAGCTGCACTGTTGAGAGAGCGCTTCTGTGACTGGGGATCGGACAGCCAATGCTGGTCCTCCGAGGCGGAAATCGCCTGCTCTCTGCTCAGCTGCTGGGATCCACAGTTCCAGAGCCGGATGAATTACCCTCCTTGATCTGcgatttcttatttatttcttatttgcaACGCGGTTTGTCTGCACTGCTCTGAGGGAGGATTGCTCCTGTCCTGGAGACGCCTGAGCGCACAGCggtgtttgttattatttcctGGCGGGGCGAGAGGGCACTGACGCGGCTATGCACGACGCGTATGAGCCGGTCCCAATCCTGGAGAAGCTGCCGCTCCAGATAGACTGCATGGCGGCCTGGGaGGACTGGCTTCTTGTGGGGACTAAACCAGGACATCTCCTGCTGTACAGGATCAAGAAAGATGCAGGCAGTAACAGGTTTGAGGTGACACTTGAAAAATCCAACAAGAATTTCTCAAAGAAAATCCAGCAGTTGTATGTGGTGTCCCAGTATAAAATCCTGGTCAGTCTGCTGGAAAACAACATCCATGTCCATGACTTGCTGACTTTCCAGCAGATCACTGTTGTTTCCAAAGCCAAGGGGGCGACTCTCTTTGCTTGTGACCTGCAGAAGAAGCTACAGCTTTATTTCTGGAAGGACCGGGATTTCTATGAGCTACAGGGGGATTTTGCAGCACCTGATGTTCCCAAGTCAATGGCCTGGTGTGAGAACTCAATCTGTGTGGGCTTCAAGCGGGACTACTACCTGATTCGGATGGATGGCCGGGGGTCTATCAAGGAGCTCTTCCCCACAGGCAAGCAGCTGGAGCCACTGGTGGCCCCACTGGCTGATGGGAAGGTAGCAGTGGGGCAGGATGACTTGACAGTGGTACTCAACGAGGAGGGGGTTTGCACCCAGAAGTGTGCCCTCAACTGGACCGATATCCCTATTGCAATGGAGCACCAGCCCCCCTACATCATCGCTGTGCTGCCCCGCTACGTGGAGATCCGCACCTTCGAGCCTCGGCTCCTGGTCCAGAGCGTGGAGCTTCAGAGGCCACGCTTCATCACCTCTGCTGGgaccAACATTGTATATGTCGCTAGCAACCATTTTGTTTGGCGGCTAGTCCCGGTCTCTATTGCAACACAGATCCGACAGTTGCTGCAGGATAAACAGTTTGAACTGGCCCTCCAGCTGGCGaAGATGAAGGATGATTCAGACGGTGATAAGAGGCAGCAGATCCACCACATCCAGAACCTCTATGCCTTCAACCTCTTCTGTCAGAAGAGATTTGATGACTCCATGCAGGTCTTTGCCAAGCTGGGTACAGATCCCACCCATGTGATTGGGCTCTACCCAGACCTACTACCCTCTGATTACCGCAAACAGCTGCACTATCCCAACCCTCTGCCAACCCTGTCTGGTGCAGAGCTGGAGAAGGCCCATCTAGCTCTGATTGACTACCTGACCCAGAAACGGAGTCACCTGGTGAAGCAGCTGAATGACTCTGACCCCTCCACCACCTCCCCCCTGATGGAGGGCACACCCACCATCAAGTCTCGCAAGAAGCTGCTGCAGATCATAGACACCACACTCCTCAAGTGTTACCTTCATACCAATGTAGCCTTGGTGGCTCCCCTGCTGCGGCTGGAGAACAACCACTGTCACATAGAGGAGAGCGAGTATGTGCTGAAGAAGGCCCACAAGTACAGCGAGCTCATTATCCTCTATGAGAAGAAGGGCCTGCACAGGAAAGCCCTTCAGGTGCTGTTGGATCAGTCTACGAAAGCCAACTCCCCACTCAAGGGCCATGAGCGGACTGTGCAGTACCTACAGAGACTAGGAATGGAAAACCTGGGAATCATTTTTGAGTTTTCTCCCTGGGTTTTGAAAATCTGTCCAGAAGATGGTCTGAAGATCTTCACTGAAGACCTGACAGAGGTTGAGACTCTGCCCAGAGAGAAGGTCCTGATCTTTCTGAAGGAAGGCTTCACAGACCTGGCTATCCCTTATCTGGAACACATAATTAAAGAATGGAAAGAGACAGGCCCTGAGTTCCACAACTGCCTGATCCAGCTCTACCTGGAGAGAGTGCAGGTGCTGATGAAGGAGTATCTCAACTCCCTGCCAGAAGATGAGGTTCCTGTGCCAGCTGGTCaggaggagggggagctggGCAAATTCCGTGAAAAGCTTCTGTCCTTCCTGGAGACGTCCACCTGCTATGAACCAGAGCGCCTCATCAGTGACTTCCCCTTTGACGGGCTACTGGAAGAGCGTGCTCTCCTTTTGGGCCGCATGGGGAAACACGAGCAGGCCCTCTTCATCTATGTCCACATCCTCAAAAACATCCGTGTGGCAGAGGAGTATTGCTGCCAGCATTACAACAGACTTACTGATGGAAGCAAGGATGTGTACCTGTCATTGTTGCGAATGTACCTGTCCCCACCTGATGTGCACTGCCTAGGGCCAATCAAAATGGAGCTGTCAGAGCCGCAAGCCAATCTGCAGGCAGCTCTACAAGTCCTGGAGCTTCATCACAGCAAACTCAACACGACCAAGGCGATCAATCTCCTACCTGCCAATACTCAAATCCGAGAGATCCGTGTCTTTCTAGAGAGCGTTCTAGAGGAGAACGCCAAGAAGAAACGCTTCAACCAGGTTCTGAAGAGCCTCCTACAGGCAGAGTTCCTCCGGGTCAAGGAGGAGCGGATTTTCCATCAGCAGGCGAAGTGTATAATCACAGAGGAGAAGACATGCCGTGTCTGCAAGAAGAAGATCGGGAACAGTGCATTTGCCAGGTACCCCAATGGCGTGGTGGTCCACTACTTCTGCTGCAAGGACCGGAACATGTGCCCCACAGAGCCATGAGCCTCTCACTGCCCACACTCATGCCCGCCACCATTCCCACCCACCCACCTTATCCCCCTCCATCCCCCACCTGGACTGTCTGAGATCCAGCACTGGGCAGCCAGAATGACACTCACACAAAGACAGATCGGCATCCTGTTCGGAGCTCAGTGCACAGACATATAGGAGCACAGGCACTATGCATGTATAAGGAACATGGAGGTGAAAGCTTTTAAACTGTAGCCCTGGAGCAAATTCCTCCCACAAAGTCTTTATAACTGTACGCCAGCTTCAAGTCTGACCGAGATGCAGGATTCTCAAGATGCACTTCAGTCGGCTCTTGTTCTGATTGGGATTGCTGCATCTGTTTCTTGGATTTCAGGAAAGATCTTTAACTTTTGTGAGCACTCACAACCATTTCCTAGACCTTTTCATGTTGTGACTGCGAGCAGTGGCTGAAACAGAGCACTTTTTGCTCTGCTATATTCATTGGTTTCTCATTTTTGGAGTtctgtaaaacacacatttaaaaggaCACTATGGAGGTTTCGTTGGAGGTTCTTGGCTAGCTGTGCTTTTGTTTCACAGCCTGTTTAAAAGGTGTATATGAAGAGAGCCCTTTCAGAACTTCTTAACCTGTTTTAAGCAGTTTTTTCTGGTAGAGATGAAGTAGTGCTTGGCTGAGTTTAGACCAGGGGTTTGTTAGTGAAGAATGCCCAATGATCTCAGGTAATCCACCATTATGTCAGGGTTTTTTCAGTAGTGGCAAAATATGATTGAAAAGAATGAACTTTGCAATTTGTTCTGAAACACTCATTGTGTGCAAATtctagatatatatagatacacttCAGCAGACTAGACAAGTCACAAATTCTCTATCATTCATTTAGGAAGGTAATTTGTTCTATGATGTTTAGAAATGGTTTGCAATTAAACTCTTACTTTCCACAGCCGAGCCTAAGACTTCTTGGAATGTGCATAATGAATTAAAAGCTCAATTTCGTTCCTTATCTTTTCAAACTGTAGATTTAACATGACCTATAAATGTGCTGATTGTGGCATTCCCAGACAAGAATTTACAGTGAaggaattaaaatgttctcaagGGATGTTGGGATAATTTAAGACCTATGCGTTCACTTTTAGCATATTATTGTCAAATTAATTCACCATTTAAAAAGGCCTGCACTAGTGTCAACATTGTGCCTTTATTTTAACTGTGTCTTATACCAATCTGACCTGCACATTTATTTCCATACAAAAAGGTTTGTCTacagtatgaaaatgaattgcttctTTACTTGTATTCACCTATTATTGTAGTGCAGAAGTCACATTCAATGGTTTTGTTAACTTAATTAGTTAGTATAAGCTGTATGTAACGTGATTGTGAAGCATACAAGCATTAACCAAGATTGTGCTTTAAAGCAGCAATATAGATTTACTATCATATGATAGAGTTGTGCAACTATTGTCCATCTCCACTTTTGTTTGCACAAGGTGAGGTGAATACAAGCATGCTGTTGTTTCAGTTCCAATAAtgagtgttgttttttcacaccCATTGTTCTAAATTTTGTAGTTGATAGCACTGATTTTTCCAAGTCACAGTTTCAAATCCTGAATCTCAGCAGGTCTTCcatttgattcttttttttttcctccaataATGAGCATAATGTAATGCATCTGGGCacctgttatttaaataaaaacaatacagaattcGCTGCATTCACGAAGGACAGTTATCTGCTACACAGCAGTGTACCTTTGGGATCTAGGAAGAGAGTCCGTGAGCTGCGTTTTCCTGAAAAGTCAGTTTTGCTGTTGATCAAATTTTATCAGAACAGACTGTTTTGAGTAGGCATAAACTTTAAAAGCTGGCAGCTTTGAATATCTTACAGCTATTGCATCTGCACTTTAATGTGTTCTACAAAGGCCTCTGACTGAGTGAATGGCACATGGATGTGAATGTGTTTCTATAGAAAGTTGCTTCTTGGCTCTGTATTGCACAGCGTGGAATGTAATGTCTTCCTCCACCCAGTTCTCCGGTTCTCCCTTTGACCTCTACCTCCAACCCCCTGTGGCCACATcatcacaaacagacacaagcAGTAAAAGTAAagcttaaaaacattatttataagcCATGCTTCGttgtttaagaaataaataaataaataaataaataaataaataaaagcatttaaattaatcgTTCATTACAAGAGGGTAGTAAAAATCAAAGTGCCGAGCCAGCTGCTGCAGGCACATGATTTCAAGGAGGAGCCAATGCATTCAAGACTGGAATCTCGTCAATGGTGTTGTGATCTTAGCTGGTATTTCACCTGCTCAGAAAGGTTTAACACTTCCCATATTAGAAAATGGGCCACACTCCAACCCAGCTTTAATCTGAGCACCTGTTTCATGGTCCTTAATAGTTACAGGAGTGTGGTTAATCAGAACTGGAATATTACACCTGTCAGCTACTTAATTTGTTtgcttagttttgttttagcaAATTTGTACAGTTAGAACAAAAAGCAGAAGGTATTGTGACCCTCCAGACAGGAGTTTGACACCTCTGTGCTAAATTGTTAGGGGGCTGACTGATTTACTGGTTTACCTGATTTAACAATAAATGGTTGCAAGGACAGCAGTACAACGCAGGAAAAACACACGTGAGACTTAAACTGGAAAcatagaaaatgtttgtttttctttttttaatagctctttaagatttaaatatatattttctaaatttcTTAATGTTATTAAAGAAACTGATTTAAACTTAAGGTGTTTGCTAGTGATCTCTGCTGCATGGCACtttagttattgttttaattactgattttattgttttaatcttaaTATTTAGACAATGTTGTGTGCAGTATAAAATGGATTGTTTAATGGCAACTCAACTCGCAATGTCAGTCCTACTATATTGTCCTAACAGAGTGTTCCCCAGGCAGAAGGGTTAATCCAATTTAGACATTGGCAACTGAAACCCTTCTTTGCCCAAATATCCCTCCAAGGCTGttacaacaataacattttgtataaaGAGAGACCTGTAATATAGAGAGTTTGGGAGGATTGTAAAAGTTTCTTAACagctgtgtaaaaataaatatatgaaaatgaatgtattgttaataGGACTGCTTTGAACAACACAGTACAAAGTATCGAAATAAAAGTTTCAAAGTGATGCCTGTTGCCTGACTTGcctgataaaaaaaattgatgGATATTTCATACTTGCAAGGAACCGTGCATCCgctttgaataaaatataaatggctTTTGATTTCCTAGTTTTATTGCCcatttcctctctcttcctttaAATTGACAGACTTAAATGCAGTATAAAGCTGACTGTTGGAAATCATTGGGaaacttttctgtgttttgttgtatttgaaatctgtattaatctgtatttgtctttttgttttcatacacaggaaaaaaaaaa

Function

symbol description
vps39 Acts upstream of or within developmental pigmentation; eye development; and vesicle-mediated transport. Predicted to be active in cytoplasm and membrane. Is expressed in brain; digestive system; head; and integument. Orthologous to human VPS39 (VPS39 subunit of HOPS complex).

NR:

description
vam6/Vps39-like protein

GO:

id name namespace
GO:0006886 intracellular protein transport biological_process
GO:0016192 vesicle-mediated transport biological_process
GO:0050790 regulation of catalytic activity biological_process
GO:0048066 developmental pigmentation biological_process
GO:0001654 eye development biological_process

KEGG:

id description
K20183 VPS39, VAM6; Vam6/Vps39-like protein vacuolar protein sorting-associated protein 39

RNA

RNA id representative length rna type GC content exon number start site end site
AMCG00000053 True 7162 mRNA 0.43 25 991040 1042603

Neighbor

gene id symbol gene type direction distance location
AMCG00000052 NA coding upstream 12496 957706 ~ 978544 (+)
AMCG00000049 NA coding upstream 92495 886906 ~ 898545 (+)
AMCG00000051 NA coding upstream 104248 886400 ~ 886792 (+)
AMCG00000048 NA coding upstream 174523 815941 ~ 816517 (+)
AMCG00000047 NA coding upstream 203191 787084 ~ 787849 (+)
AMCG00000054 NA coding downstream 96440 1139043 ~ 1164404 (+)
AMCG00000055 NA coding downstream 200595 1243198 ~ 1294765 (+)
AMCG00000056 NA coding downstream 318774 1361377 ~ 1383054 (+)
AMCG00000057 NA coding downstream 650549 1693152 ~ 1719606 (+)
AMCG00000066 NA coding downstream 698206 1740809 ~ 1781771 (+)
G147405 NA non-coding upstream 49129 940858 ~ 941911 (+)
G147314 NA non-coding upstream 505579 482114 ~ 485461 (+)
G147313 NA non-coding upstream 517533 470695 ~ 473507 (+)
G147292 NA non-coding upstream 604087 386290 ~ 386953 (+)
G147288 NA non-coding upstream 634052 356772 ~ 356988 (+)
G147466 NA non-coding downstream 146205 1188808 ~ 1189042 (+)
G147551 NA non-coding downstream 446977 1489580 ~ 1492313 (+)
G147564 NA non-coding downstream 543454 1586057 ~ 1586324 (+)
G147565 NA non-coding downstream 545474 1588077 ~ 1588295 (+)
G147579 NA non-coding downstream 570707 1613310 ~ 1615951 (+)
G147311 NA other upstream 492529 449652 ~ 498511 (+)
AMCG00000032 NA other upstream 736599 231336 ~ 254441 (+)
AMCG00000025 NA other upstream 886678 55439 ~ 104362 (+)
AMCG00000026 NA other upstream 953265 28694 ~ 37775 (+)
G147416 NA other downstream 20482 1063085 ~ 1116950 (+)
AMCG00000073 mta1,LOC107679789,LOC107666257,LOC107600838 other downstream 993420 2036023 ~ 2058770 (+)
G147726 LOC104962440 other downstream 1361127 2403730 ~ 2403972 (+)
AMCG00000094 NA other downstream 2648169 3690772 ~ 3699093 (+)
AMCG00000093 srp14,LOC106610862 other downstream 2678382 3720985 ~ 3724316 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
zebrafish (Danio rerio) XLOC_011741 vps39 coding NC_007128.7 CM002901.2 50074372 ~ 50114272 (+)
grasscarp (Ctenopharyngodon idella) CI01000314_00003811_00027858 VPS39 coding CI01000314 null 3783 ~ 27858 (-)