RNA id: XM_026925268.2


Basic Information

Item Value
RNA id XM_026925268.2
length 6733
RNA type mRNA
GC content 0.46
exon number 24
gene id upf1
representative True

Chromosome Information

Item Value
chromosome id NC_047615.1
NCBI id CM018561.1
chromosome length 21248730
location 16071106 ~ 16088518 (-)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome
species striped catfish
(Pangasianodon hypophthalmus)

Sequence

TGTTCACGTCACCATTTCGAGTGGGAGTTGAAGCTTCCTTTCGAAGCCGTACGCGTTCATTCGTGATAACGCTTTTGAGTTTAAATCAAAACAATATTGCGAGCGTGTTcgttttttaaaacatattcattgtgtaagtgtttgtggggtttttttgtttgttttttttttttatttgtgaaagcGGACCTTGCTGGTTGGGGGATAAAAATGAGCGTAGAGGCGTACGGGCCGAGCTCGCAGACTCTCACCTTCCTGGACACGGAGGAAGCGGAGCTGCTCGGAGCCGACACGCAGGGCTCGGAGTTCGAGTTCACCGACTTCACCCTGCCGAGCCAGACTCAAACACAAGGCCAAACCCAGAGTCAGCTCGACAACCAGGTGAATGGACCTGAGGGAGTTCTGCAGAACGGCGATGATGCTGTGGTGAAAACCAGTCAACTTCTGGCAGAGCTGAATTTcgaagaggatgaagaggacaCCTATTACACCAAGGATCTCCCTGTGCATGCCTGCAGTTACTGTGGTATTCATGATCCTGCCTGTGTGGTGTATTGCAACACCAGCAAGAAGTGGTTCTGCAATGGACGTGGCAACACCTCTGGCAGCCATATTGTCAACCATTTGGTGCGTGCCAAATGTAAGGAGGTGACCCTGCATAAAGATGGTCCTTTGGGGGAAACAGTGTTGGAGTGTTACAACTGTGGCTGTCGCAATGTTTTCCTCCTGGGCTTCATTCCAGCCAAGGCCGATTCTGTCGTGGTGCTCCTGTGCAGgcAGCCATGTGCCAGTCAAAGCAGTCTGAAGGACATTAACTGGGACAGCTCCCAGTGGCAGCCTTTGATCCAGGACCGGTGCTTTCTGTCCTGGCTGGTGAAGATCCCGTCTGAGCAGGAGCAGCTCAGGGCACGCCAGATCACCGCTCAGCAGATCAACAAACTGGAGGAGCTCTGGAAGGAGAATCCAACAGCAACACTTGAGGATTTGGAGAAGCCTGGTGTGGATGAAGAGCCTCAGCATGTTCTGCTGCGATATGAAGATGCCTACCAGTATCAGAACATCTTTGGCCCATTGGTCAAACTGGAGGCAGACTATGACAAGAAGCTTAAAGAGTCCCAGACCCAAGACAATATAACTGTCAGGTGGGATTTGGGACTGAATAAAAAGAGGATTGCTTATTTCACCCTTCCCAAGACGGATTCAGGTGACATGCGTCTTATGCAAGGGGATGAGATCTGCCTGCGTTATAAGGGAGATTTGGCTCCTCTCTGGAAGGGGATTGGACATGTCATCAAGGTCCCTGATAACTATGGAGATGAGATTGCTATAGAGCTGAGGAGCAGTGCTGGAGCTCCCGTGGAGGTGCCCCACAACTTCCAGGTGGACTTTGTCTGGAAATCCACTTCCTTTGACCGCATGCAGAGTGCCCTGAAAACATTTGCGGTAGACGAGACCTCAGTGTCTGGTTACATCTATCACAAGTTGCTTGGCCATGAGGTGGAGGATGTGATCATTAAGTGCCAGTTACCCAAGCGCTTCACTGCCCAGGGCCTGCCTGACCTCAACCACTCACAGGTGTATGCTGTGAAAACGGTGCTCCAGCGTCCCCTCAGTCTGATCCAGGGGCCTCCTGGTACTGGCAAAACTGTTACCTCAGCAACTATTGTTTACCATCTGGCTAGACAGGGCAACGGGCCGGTGCTGGTATGTGCTCCCAGCAACATTGCAGTGGACCAGCTGACAGAGAAAATTCACCAAACAGGACTGAAAGTGGTGCGTCTCTGTGCCAAGAGCCGAGAGGCCATTGATTCTCCTGTGTCCTTCCTGGCTCTGCACAACCAGATTCGCAACATGGACAGCATGCCAGAACTGCAAAAGCTGCAGCAGCTGAAGGATGAAACAGGAGAGCTGTCTTCCTCGGATGAGAAGCGCTACAGGGCCCTGAAGCGCACTGCAGAAAGGGAGCTACTCATGAATGCAGATGTGATCTGTTGTACTTGCGTGGGTGCGGGTGATCCTCGTCTGGCTAAAATGCAGTTCCGCTCCATCCTGATAGATGAGAGTACCCAGGCTACTGAGCCAGAGTGCATGGTTCCTGTAGTGCTGGGAGCCAAGCAGCTGATCCTGGTGGGTGATCACTGCCAGCTAGGTCCAGTGGTCATGTGTAAAAAGGCTGCTAAGGCAGGTCTGTCCCAGTCTCTTTTCGAGAGACTGGTGGTGCTGGGCATCAGACCCATCCGTCTACAAGTGCAATACCGTATGCACCCTGCACTCAGCGCTTTCCCCTCCAATATCTTCTATGAAGGATCTCTCCAGAACGGAGTCACTGCTGCTGACCGCATCAAGAAGGGCTTTGATTTCCAGTGGCCTCAGCCAGATAAGCCCATGTTCTTCTATGTGACACAGGGCCAGGAGGAGATTGCCAGCTCAGGCACCTCCTACCTCAACAGGACTGAGGCTGCTAATGTGGAGAAGATCACCACTCGCCTTTTGAAGGCCGGAGCCAAACCTGACCAGATTGGTATAATCACTCCCTACGAGGGCCAGCGCTCCTACCTGGTGCAGTACATGCAGTTCAGCGGTTCCCTTCATACTAAGCTCTACCAGGAGGTGGAGATAGCCAGCGTGGATGCCTTCCAGGGCCGTGAGAAGGACTTCATTATTCTGTCTTGTGTCAGAGCCAATGAGCACCAAGGCATCGGCTTTCTTAATGATCCACGCAGGTTGAACGTTGCCCTCACCAGAGCCAGGTATGGTGTGATCATTGTGGGGAATCCTAAAGCTCTGTCTAAGCAGCCACTCTGGAACCACCTGCTGAACTACTACAAGGAGCAGAAGGTTCTGGTGGAGGGGCCTCTCAACAACCTGAGAGAGAGCCTCATGCAGTTCAGCAAACCTCGCAAGCTCGTTAACACCATCAACCCTGGAGCTCGTTTTATGAGCACTGCCATGTATGATGCCAGGGAGGCCATGATCCCCGGCTCAGTGTATGACCGCAGCAACACTGGTCGTCCATCGAGCATGTATTTCCAAACTCACGACCAGATTGGGATGATTGGTGCAGGGCCGAACCCTATGGCCTCCATGAACATTCCCATACCCTTCAACCTGGTCATGCCCCCCCTGCCCCCACCAGGCTACCTGGGCCAGATTAATGGCCCGGCTACTGGTCGTGGTGCGTCAAAGGGAAAGCCAAGTGGGCGCGGAGGACGGCAGAGGAATCGTGGCGTGGGTAACCATGGCAGCGGGCAGACCAACATGGCAAACAGCCAGGCCAGTCAGGATCTGGTATCTCAGCCCTTCTCTCAGGGTCCCCTGACCCAGGGCTACATTACCATGAGCCAGCCCTCACAGATGAGCCAGCCAGGCCTGTCCCAGCCTGAACTTTCCCAgGACAGTTACCTGGGTGATGAGTTCAAGTCGCAGATGGATGTGGCTCTGTCCCAGGATTCCACTTACCAGGGTGAACGGGCATACCAGCATGGAGGAGTGACCGGACTCTCTCAGTACTAGAGTGTTGTTGGAACGGGAGCTAGGCCTACGCTGAGCTTAGTTCATCAGCATTTTAAATCTgggtaaatataaaaaaagaacaaacatggATGCCCGTTTTCCACTGTTACAACTGAAGCACCATGGTGTGAGAACAACAGGAGAGAATCAAACCAATCACGTGtgaaaaaagagggagaaaagcagGATAAGAAAAGAGGGAACGAAAGAGAGTGGAGGGAGGAAACCACCCCACCACTCGCTAAGGATGggaaggaggagagaggagcAGACGCAGCATAGGAGGAGACGATGTAGGAGGGAAATCAAACCGAGATCTTCGATCTGCAACTCCGCATAGTCGAGGCGCCTCCTGGGGAGCAGGGCAGTCCCTTACCTGCCTCCTCTCTCTCGCCAGGCTGCAGCCGGCAGCCGCAGACCTCGCTCTGCCACCCGAGACGGAGAGAAGACGAAGTTCTCTTAAAACTACCTGCAAAAAAAACGCCACGCTTGCTCTGTCGTCTCCACAAGCTGAAAGATGAGGTGacgtctttaaaaaaatgatcaaataaagatattttttaaaaaaaacactttcaagCAGCTGATTTTGGGGAAAATTTTCCCTTCAAAGTTGGAATCTGACTTTCAGATATTACCACCAAACATCTTTGAGAGGATGGGGAAACATCTCTGGGCGGAGGGTTGTGCTTTtacgcattttttttttttttattttattttttttttttttcttttttttttttgtggtggtggtggtccCATCTTTACAAATGGTGCTAGGAGTCTCTGAAGAAAGATTCAACTTTGAGGAAAGTTTTCTGATTGAAGGTTGTGGAGTAGTGGTTCAGAAATGGAACGGCTCTGAGAGATGTCgcctgctctgggtgtgtgacCAATGGAAAAGATGGGGAGTCTTAACAAATGgctttgtgatattttttaacaaaatggcaaACTGGAAGGGTTGAGAGATTTGAAGTTTATCATTTTTTGCCTcaccattttaaacaaattgttTTGAACCCAGATAAACAATTGCAGCAGAACCTAAATTTAGAGATAGGTCATTAGTGGCTTGTTGATGTCTCTATATGGAAAACATGAAGTCATAGGTCCCCAAGAAAATGAGCCAAAAAGCCAGTGGTCAAGCCACTAAAGTTAACCTGTCGCATACCATACGCTCACAGGACCGCTGGAGATTGAACCCGGGGGGCTAATACAAGTTTGAAAAGAGTTTAGAGAATTATCTCAATCTGTAGGAAGATTAAAGCGCTGCTCTCACGTTCAGCAGCAGTTCTGGCAAGTAGCATATTGGTTATGGTCAGTTCCTCTGGCTTCAGTACCGGCATTAAAATCTTTATGCTTCCACTACAGGCAGTGCTGCAAAAccaagatttattttctaaatcaCTCCACCTATTTAGTAAAATTCATAATAATGCACCACATATCAGATTGAGTTCTTGAGTTAAATTATTCCTATACATGAGTTTGAGCCATGAGTTAAATACAGCCGAAAATCACAAAAGTGGCCGTTTGTTAAAGGGTAAAGGGCAGACAGGTGGGATTCTCGCTGTTTGTGTCCGTTTCCCACAAGCAGACTGAAAGAGGCTGCTGTACTCGTCTCTTGCTTACTTGGATGCCAGTGTGTGCGTAGATGGTAGTGTTCTGCTAAGGAGGTTGTGTATGTGCCTCCATATTAATTGTCTCTCTTGTTTTGTGATtaatagtttgtttgtttttttttcttcccccttGTTGGTTGTTGAAGTTGCTTTTCCCCCTATTTActgtctttattattttaacaccTAATTGCATTGTATTTCATTTCTGTAGTCTAGATATGAATGTGAGGTGTACCACATTATCCACTTCATGATCTAAGACTattcataaaattttttttttttttcgtttctttcttttctaaagCTCTGCTCGTAGAATGCTTTGATGCAGCAACATGTGATGCCTTGTCATTTTCATTAACCCTGGAATGTTCATGCCTTGCAGTTATTCCTTGCCTAGTGGCACAATAGCTTGGCATTACTACCTTTTTAGTCTTGGCtctaaactggaaaaaaaaaacaaaaccaaaaaaaaaaaacctttccctATTGGAGTTACAATTGTTCATTTAAAGCGTTTTGTTGTCTAATGGATTTATAACAAATTGCAAAAAGATTTTGTCATTTCTGACATTCACTGCTTGTGTGCATAGCGCTTTCATGTTATTTATAGTTATTCTCATTGGTAGTATCAAAGCTAAATGTAGGCTATACATCCAAAATTAAACAGGGAACTAAATATCCAGAACATAGCTTCTTCAtgttctcatttttaaaaaatcaattccTCTCCCATGATTTGAATGGGTTCCTTTACTTTGGTGTACTTGGTAAGCAGATACTGCCCATAtcaataataaaagttttttttttcctcttttttgtgTGATATGGCCTAGAGCAACAACAACCTGATAGAGACTGATGAACACCCATTATACGGAGGTTGTTCGGGTGGTTGGATAGACACTGTGTTTACTCACTTGAATGCTAAAACTTCAGTACTCTGATATGGCCATGTCAGACTCTCATACTTAATGACAGCCTGTTGAGATTGCAATCAGAAGAAAATTACAGAGGGGACTAATACTGACAAAATAGATGAAGTACCCTGACCACCCTGAGGGTAGGAAGACTTTAAATTGAATCAAAGGGTATAAAAGACCAGAGATTAAGTTTtctttaatggaaatatttccCCACAGTATGTAATTCTTGTAATGTTACTACAATAAATGTTGCTTTATTTCACTCAAGAAGACTGGTCGTTTGAGTATGTATTGTCTTCGAGTTATTAAATATTCTAGTGAAATGTAAAAATCCTATTTGAAATGAGACCATAATTCTATAAAATTAGACCAATTTTTTGGACTAAGAGTGTAGTATGATTTGAAACATACTGTTGCATTTCTTACATCTGTCACATGGTTTCAGCACTTCTCATTACACTGATTTGATTTAGAAACTCGAAACAAGCATAAGCTAGCTACCACTATTGCCTGTGGTGTACAAAAGATTGTATACCCTTCAAATCCTCAAGACTTTTAATGTGGGTTAGACAATTTTACAGATGTTCGTTTCAAAATGTGTATGTCAAGATATTAATCATGTAATTATTAAACTTatatttctgaatgtgtgtTAAA

Function

GO:

id name namespace
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay biological_process
GO:0009790 embryo development biological_process
GO:0005737 cytoplasm cellular_component
GO:0005524 ATP binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0008270 zinc ion binding molecular_function
GO:0004386 helicase activity molecular_function

KEGG:

id description
K14326 UPF1, RENT1; regulator of nonsense transcripts 1

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
TU380538 lncRNA downstream 21463 16049442 ~ 16049643 (-) True G321347
TU380518 lncRNA downstream 29365 16040881 ~ 16041741 (-) True G321330
XR_004576914.1 lncRNA downstream 243762 15811353 ~ 15827344 (-) True LOC117595737
XR_003403425.2 lncRNA downstream 357934 15687082 ~ 15713172 (-) False LOC113533563
TU380540 lncRNA upstream 10350 16098868 ~ 16099238 (-) True G321349
TU380546 lncRNA upstream 99458 16187976 ~ 16190570 (-) False G321354
TU380548 lncRNA upstream 99458 16187976 ~ 16223314 (-) True G321354
TU380547 lncRNA upstream 103834 16192352 ~ 16223314 (-) False G321354
TU380672 lncRNA upstream 285992 16374510 ~ 16375343 (-) True G321465
XM_026925564.2 mRNA downstream 2545 16041828 ~ 16068561 (-) False LOC113533416
XM_026925563.2 mRNA downstream 2545 16041828 ~ 16068561 (-) True LOC113533416
XM_026925307.2 mRNA downstream 142039 15924221 ~ 15929067 (-) True polr2ea
XM_026925125.2 mRNA downstream 209624 15854503 ~ 15861482 (-) True zgc:85843
XM_034297689.1 mRNA downstream 422362 15594435 ~ 15648744 (-) False LOC113533480
XM_026925366.2 mRNA upstream 2006 16090524 ~ 16094854 (-) True pgpep1
XM_026925155.2 mRNA upstream 40183 16128701 ~ 16131801 (-) True LOC113533206
XM_034314864.1 mRNA upstream 43051 16131569 ~ 16132462 (-) True LOC117599986
XM_026925765.2 mRNA upstream 52246 16140764 ~ 16143363 (-) True nmrk2
XM_026925766.1 mRNA upstream 52246 16140764 ~ 16143092 (-) False nmrk2
TU380217 other downstream 346750 15687258 ~ 15724356 (-) False LOC113533563
TU380215 other downstream 353611 15687258 ~ 15717495 (-) False LOC113533563
TU379938 other downstream 841850 15227472 ~ 15229256 (-) False LOC113533479
TU379789 other downstream 1325619 14731912 ~ 14745487 (-) False theg
trnaw-cca_17 other downstream 4522667 11548368 ~ 11548439 (-) True trnaw-cca_17
TU380669 other upstream 269056 16357574 ~ 16367004 (-) True G321462
XR_003403441.1 other upstream 531115 16619633 ~ 16619734 (-) True LOC113533663
trnal-uaa_3 other upstream 885170 16973688 ~ 16973770 (-) False trnal-uaa_3
trnal-uaa_4 other upstream 992503 17081021 ~ 17081103 (-) True trnal-uaa_4
TU381420 other upstream 1411547 17500065 ~ 17500832 (-) True G322080

Expression Profile