AMCG00006067 (upf1,LOC105907049)


Basic Information

Item Value
gene id AMCG00006067
gene name upf1,LOC105907049
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 15544838 ~ 15559349 (-)
genome version AmiCal1_2021_bowfin_Genome

Sequence

>AMCG00006067
CGAATTGGTGTGGGAGTTGGAGCTCTcgggctgtgtgtgtttcagtttgaTTTCTGATTCGGTTCGACTGCTGTTTGGGCTGAAATCCAGCGCGGCGCCGGGACAACACACACCGGAACCGGGAAACCTTGCGGAGTCCGACACGACCGCCCTTCTACTCCCCCGAAACAGAGGCTGTAAAACCCCCGTCGCTGGAGCAGAAATGAGCGTGGAGGCGTACGGGCCGAGCTCTCAGACTCTCACCTTCCTGGACACGGAGGAAGCGGAGCTGCTGGGCGCCGATACCCAGGGCTCGGAGTTCGAGTTCACCGACTTCACTCTGCCCAGCCAGACCCAGACGCAGGGGCAGACCCAGAGCCAGCTGGACAACCAGGTGAATGGCCCCGATGGAGTTTTGCAGAACGGTGCGGTGGATGATGCTGTTGCAAACACAAGCCAGCTCCTCGCAGAACTGAACTTTGAAGAAGACGAAGAGGATACTTATTACACCAAGGACCTCCCAGTGCATGCTTGCAGCTACTGCGGTATCCATGATCCGGCGTGTGTGGTATACTGCAACACCAGTAAGAAATGGTTCTGCAATGGCCGTGGGAACACCTCTGGCAgCCACATTGTAAACCACCTGGTGAGAGCGAAATGTAAAGAAGTAACTCTTCACAAGGACGGGCCCCTGGGGGAGACAGTGCTGGAGTGCTACAACTGCGGCTGCCGCAATGTCTTCCTCCTGGGCTTCATCCCGGCCAAGGCGGACTCTGTGGTCGTGCTGCTGTGCAGGCAGCCGTGCGCCAGTCAAAGCAGCCTGAAGGACATTAACTGGGACAGCTCTCAATGGCAGCCTCTGATCCAGGATCGCTGCTTCCTGTCCTGGCTGGTGAAGATCCCTTCGGAGCAAGAGCAGCTGAGGGCCCGGCAGATCACCGCCcagcagatcaacaagctggaGGAGCTCTGGAAGGAAAACCCCACCGCCACCCTGGAGGACCTGGAGAAGCCCGGAGTGGACGAGGAACCCCAGCACGTGCTGCTACGCTACGAGGACGCCTACCAGTACCAGAACATCTTCGGCCCGCTGGTCAAGCTGGAGGCAGATTATGACAAGAAACTAAAAGAGTCCCAGACCCAGGATAATATTACAGTTAGGTGGGATCTAGGACTGAATAAAAAACGGATTGCTTATTTCACCCTCCCCAAGACGGATTCAGGTGATATGCGTCTGATGCAAGGAGACGAGATTTGCCTGCGGTACAAGGGAGACCTGGCGCCCCTGTGGAAGGGAATTGGGCACGTCATCAAGCTGAGGAGCAGCGTGGGGGCCCCCGTCGAGGTGCCACACAACTTCCAGGTCGACTTTGTCTGGAAGTCCACCTCCTTCGACAGAATGCAGAGCGCCCTGAAGACATTCGCAGTGGACGAGACTTCAGTATCCGGGTACATTTACCACAAACTGCTGGGACATGAAGTGGAAGACGTCATTATTAAGTGTCAACTGCCAAAACGCTTTACGGCACAGGGGCTGCCCGATCTAAACCATTCTCAGgtGTACGCAGTGAAAACTGTACTTCAGAGACCCCTGAGTCTTATCCAAGGACCCCCCGGGACAGGAAAAACAGTCACCTCTGCTACCATCGTGTACCACCTGGCCAGGCAGGGCAATGGCCCGGTGCTTGTGTGCGCCCCGAGTAACATCGCCGTGGATCAGCTGACGGAGAAGATCCACCAGACTGGACTCAAAGTTGTGAGGCTTTGTGCCAAAAGCCGAGAAGCTATCGATTCCCCGGTGTCTTTCTTGGCTTTGCACAATCAGATCCGCAATATGGACAGcatgccaGAACTTCAGAAGCTCCAGCAGCTGAAGGATGAAACCGGGGAGCTGTCGTCTGCGGATGAGAAGCGCTATCGGGCTCTGAAGCGCACGGCCGAGAGGGAACTCTTGATGAATGCAGATGTGATCTGCTGCACCTGTGTGGGAGCCGGGGATCCACGGCTGGCCAAGATGCAGTTCCGCTCTATCCTGATTGACGAGAGCACCCAGGCCACTGAGCCGGAGTGCATGGTTCCCGTGGTGCTGGGAGCAAAGCAGctgaTTCTCGTTGGGGACCACTGTCAGCTGGGGCCCGTCGTGATGTGCAAGAAAGCAGCCAAGGCCGGCCTGTCTCAGTCCCTGTTCGAGCGCCTCGTGGTGCTGGGCATCCGGCCCATCCGCCTGCAGGTGCAGTACCGCATGCACCCCGCCCTCAGCGCCTTCCCATCCAATATCTTCTACGAGGGCTCTCTCCAGAACGGAGTCACTGCCGCTGATCGAATCAAAAAGGGATTTGATTTCCAGTGGCCACAGCCAGACAAACCCATGTTCTTTTATGTGACTCAAGGGCAGGAAGAGATCGCCAGCTCTGGGACCTCCTATTTAAACAGAACTGAGGCGGCCAACGTGGAGAAGATCACAACCAAGCTTTTGAAGGCTGGAGCCAAGCCAGACCAGATCGGCATCATTACTCCATATGAGGGCCAGCGCTCCTATCTGGTGCAGTACATGCAGTTCAGTGGCTCTCTGCACACCAAACTCTACCAGGAGGTTGAGATTGCCAGTGTGGACGCCTTCCAAGGCCGTGAGAAAGACTTCATCATCCTGTCCTGTGTCAGAGCCAACGAACATCAGGGCATCGGGTTTCTGAATGATCCCCGTCGTCTCAATGTTGCTCTCACAAGAGCCAGATATGGTGTGATTATTGTTGGAAACCCAAAGGCTTTGTCTAAGCAACCCCTGTGGAACCACCTGCTGAACTACTACAAGGAGCAGAAGGTCCTGGTGGAAGGACCCCTGAACAACCTGAGGGAGAGTCTCATGCAGTTCAGCAAGCCCCGCAAGCTCGTCAACACCATCAACCCGGGTGCCCGTTTCATGAGCACAGCGATGTATGACGCTCGGGAAGCCCTGATTCCGGGCTCAGTTTATGACCGGAGCAGCACAGggCGTCCGTCCAACATGTACTTTCAAACCCATGATCAGATCGGGATGATTGGCGGTGGGCCCAGCCACATCGCTGCCATGAACATCCCCATCCCCTTCAACCTGGTCATGCCACCGATGCCGCCTCCAGGGTACCTGGGGCAGGCGAATGGCCCGGCAGCAGGCAGAGGAGCCCCAAAGGGTAAAGCTGGCCGCGGAGGACGCCAGAGGAACCGTGGGATGGGCAATCAGGGCGGCAGCCAGGGCAACCTGCCCAACAGCCAGGCCAGTCAGGACGTGGTCTCCCAGCCCTTCTCCCAAGGCCCCCTCACTCAGGGCTACATCTCCATGAGCCAGCCGTCTCAAATGAGCCAGCCAGGCCTGTCCCAACCAGAGCTGTCTCAGgacAGTTATTTGGGTGATGAGTTCAAGTCCCAGATTGATGTGGCGCTGTCACAGGACTCGACTTACCAGGGTGAACGTGCATACCAACATGGCGGGGTGACTGGACTGTCACAGTTGTGGGAAGAGGAGCTAGGCTTGAGATGAGCTTAGTTCGTCAGCATTTTAATCtgggtaataaaaaaaaaacaaaaaatggataCCTGTTTTCCACTGCTACAACTGAAGCACCACTGTGTGAAAGCAACAGGAGGAGTGAAACCAACCAatcacgagagagagagaggagagagagacagacagaaagacggacagacagggagagaaagaccACTGCTAGCACACTGAGACAGAAGGGAAGGAGAAAATGCGGAGTATGTGGTGGCGCTGATGCAAAAGAGGAGGCTCTGGTCTCACATCGAAAACAACGTTCCTCCCTATGAAAGAagcccccaccccaccctgaTCCCCCGTCCcgctcccctcctcccccccggGAATGACCTGTTGACTGAGGTCCTTGCTCTTCTGGCAGAGATAGAGGGGAGAAGGCCTCAGGCAACGTGGAAACTCATTCCATCGCCTGTTCCACAGAGAAGCGGGGGGAGTTTATCGCTTAAAGCAGACCAAGAACATTTTTAACCTCAAAGTTGATCTGTTCACACTCAACAGAGCTCTCGGTTCAGTAAAACGCATACCAAATATTGGGGGTAGCAATATTGAGCAGATAAAAGCTGCGTCTTTGTTACACCAAACAAGCAAAGcagtataaaaacacaaacgaCCCCGATTCTGGTTCAACTTTGAGTTGCaaaagttttctgttttaagtCCGATAAAGAAATTCTGAATTGGAAACGCCTTTGAATGCGCTCGGATTTTCACTGGCTTTCTAAACAGGTCTTTCACGAGGTGGCTTACTGGCGTCCGGAGGTGAACTGCACTGGAGACACAAAGAGAGGCTCGTCTCTTTAAGATCTGAGCGGTGGGACTGAGAGATCTGTAGTCGTGAGACAATTTTCCGAAGTCACTTTCTTCTAGAAAAACCAGCATCGAAGAGTACTAACTTGGTGTAATTTTGAAGTTGTGGCTTATGGCTTATTGATCTTCTTTAATGAAGGAAAGCAGTGAATGCTAGTGAAGATGTGGCCTCCgagctacaaaaaaaataagaaaaaaagagggTTTTCGATATTTTAAATGCTCTGTACGCTTATAGCGGCTACTGTCCGAACTCGGAAGGAAGGGGTTTGCAGAAACCGATTGCCTTCGGCTGTAAGAGTTGCCTGCTTTGAGCAACTCCCTAGAAAAAGACAccagggaaagagagggaggcgatatatatttatttatctatatatatatatatttacggGAGTCATACAGGTGAAGTTTCAGCAGGTAGATGGATAACAAATGGGGAAAGAGTTTGAAAAGGAAGGTGGCTGAATGGATTTCAATTCCaggaaaggttttgttttttgtttgtttgtatcttttCATAGAGGTTTGCTGCTCTAGATTTGTGTGTATCCTGCAAAGGCCAAAACCTTTTCCAGGTGGTAAAGTGGACCCATCTAATTTCCAGGGATGCACACACGATTTCCAACCGAAATGCTCAAACCTTAAAAATGACAAGTAGCATCAGCCTTTTGGTCCATTCGGAGTGAATTTCACATAGATTAGTGagtttttgcttttcttgtaggttttttttttttttttttttaagtcaggtTTGGTTTTAGTAATGCTGCCTGTCTACAAATAAAGAATTAGATTTAATCtcttgcacttttttttttgtgtgtgtgtaccgcTTTAGTGAGCttaccttttcatttttcatccaGACATCCAAAGAATTCTTGCGCACAGCCCGAAGTTTGAATTTTCTAATTGGGATCTTCTAGTCTGTTTTTAACAAGGTTGAAACAATTTGATTAAAGGTGGAGGATGGAAGTGGAAGTACATCCTGTATCCTAAAAACACAAGCTCagactttttatgtattttttattgttataaaaGAGTATCCATTTCAAGAGGTTGCTTGTAGAGTCTTAGGTTACCCCTTGCCTCCGTAGAATAAGAGGTCTGTATTTCTCAGATGAAAGGATGGAGAATAATCAGTGCCTATTACTGTACTAAGACTGTTACTTTAAGGATGATTTGAACATGATTGTGGTTTCATTTATAAAGCACCACAACCTCTTGCCAATAAGGAGTCCAAAATTTTGAATGTAGGGTGAAGCATCTGCACCAGCTAATCCAACTGTAGGATGAACACCAACTGATCCTGCAGTTTGTTTCCCCCgttttgttcttaattttttttaataacaagcAATACTAGATGAAAAAATCACAGTCGAAATTTGatgcttctttatttatttttttccattgctgGTTGTAATTTCTGAAGGGCAGAGAAAtacaggccaccttcctcctgTCAGGAGTTaccattaacaaaaacagactggcCGAAAGGGCTTTTCTTTCATCacttctcattttattttattttttaagttttgttttgcttctcaGTAGTTTGTAGACTGCAGTTTGCCTATTTAGTAGAGATCTGGAGTAGATTTCTGTGACTCCCATCCTTTTGTGAACTGTGATCAAGTGATGTAATAACCCCCTTCCTCTCCCCCACCTTTTCACTGGTTGCAATgattgctttgatttgtttttgcagttttatttttctctgtagcagcaagtgatgtttttttgtttttttttgtatgctgGAGAAATCGGTGCATTCCTGCATTTGATGGAGATGGggaaagtatttttgtttgtttttgtccaagTTGTTATAAAAGCTGTCTTTAATAAACTATCATAAGTAGTTTTTGCCATGCGGAAGACTTATTCTTGACTGTCCACTGATTGGGTTTTCACCGTTGACCACCTAACCATTGTAGTCCTGTTTTAGAGCCATCAGCTGAAGAGctttaaatatagatttgatgTCGCTCAAGAGTTGTACAATTCTAGTAAACAAAACATGTGGATTTATTGTTTCCGGACATTGAGCACAGTAGTATATTTAGTTGTGTTCACAGATTGACAATCACGCTTGCTTCACGATCATGAAATCTCGTCTTGTAATAGTTCTACAGCTACTGTACGGAAAGTGAAAACGCCACAGCATGCTTACATCCAACTGATTGTGGGGAATACTATGGATTTTCAAACCTATGATGTGCTTCTTCAATTGTATCAGTTTTTGTGTGCGTGCCCCCTGCCCAGGCAGAAGACAAAACAACCGAAACTGAAAGGGAGGAATCCGTATAATGCATCTCTATTGTCGACATTCAGCGGATGCAACTCCTTGccttggttgtgtgtgtgtgtgtgtgtgtgtgtgttcggtAGAACAGCCACCAGCCACTGTTGTGCATCTTACAACAGGATGTGGGCGGGGGACTTTGCATTACTTTGCTTTGTGTGCAACGTGTATAGGAGACCTTGCTGGGAACATGGTATTTGAAAGGAAAGCAACCTATTTGAAACAGACTGGGGACAGTGGGCAAAGGAGTGAACCAGGAGAGATTTGGAAGTCTGtaatgggattttgtttttctttggcggagatttttttttgtttctttactgggggtgggaggggagaTCTGAACTCACCAGGAATGGGgagattgtatttttgttgctgTGGAAATTGTTTGCCTTCAcctatgcttttttttttttttcttcttcttaatctGAAATAACCCACCTGTAACACCTTAATCTCATTCCTGTAAATTTAttgaaacttttaaaacaaattaataaaggttgcttctcttta

Function

symbol description
upf1 Predicted to enable RNA binding activity and RNA helicase activity. Involved in nuclear-transcribed mRNA catabolic process. Acts upstream of or within chordate embryonic development and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Predicted to be active in cytoplasm. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase).

NR:

description
PREDICTED: regulator of nonsense transcripts 1

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

RNA

RNA id representative length rna type GC content exon number start site end site
AMCG00006067 True 7190 mRNA 0.48 24 15544838 15559349

Neighbor

gene id symbol gene type direction distance location
AMCG00006068 NA coding downstream 15514 15496753 ~ 15529324 (-)
AMCG00006082 NA coding downstream 56157 15483162 ~ 15488681 (-)
AMCG00006079 arrdc2,LOC106573914 coding downstream 64520 15469241 ~ 15480318 (-)
AMCG00006081 gamt,LOC107747770,LOC107597217,LOC107685360,LOC107553529,LOC107757934 coding downstream 143874 15397252 ~ 15400964 (-)
AMCG00006080 NA coding downstream 154257 15378222 ~ 15390581 (-)
AMCG00006069 pgpep1,LOC103360783,LOC104958139 coding upstream 6113 15565462 ~ 15574687 (-)
AMCG00006075 NA coding upstream 214329 15773678 ~ 15776508 (-)
AMCG00006085 NA coding upstream 218858 15778207 ~ 15784001 (-)
AMCG00006086 NA coding upstream 229998 15789347 ~ 15818856 (-)
AMCG00006087 NA coding upstream 281563 15840912 ~ 15877424 (-)
G156049 NA non-coding downstream 112908 15427308 ~ 15431930 (-)
G156048 NA non-coding downstream 120988 15417978 ~ 15423850 (-)
G156028 NA non-coding downstream 177197 15366104 ~ 15367641 (-)
G156014 NA non-coding downstream 214292 15272813 ~ 15330546 (-)
G156003 NA non-coding downstream 226661 15207520 ~ 15318177 (-)
G156104 NA non-coding upstream 22508 15581857 ~ 15584766 (-)
G156113 NA non-coding upstream 56213 15615562 ~ 15615787 (-)
G156203 NA non-coding upstream 387859 15947208 ~ 15947527 (-)
G156207 NA non-coding upstream 435438 15994787 ~ 16000039 (-)
G156225 NA non-coding upstream 503384 16062733 ~ 16063072 (-)
G156088 rps15,LOC107680474,LOC107685215,LOC107578086 other downstream 53196 15433432 ~ 15491642 (-)
AMCG00006102 slc5a5 other downstream 536859 14998500 ~ 15007979 (-)
AMCG00006043 NA other downstream 760558 14782506 ~ 14784280 (-)
AMCG00006037 rpl36,LOC106560598,LOC107678109,LOC107741803,LOC107744644,LOC107577535 other downstream 861858 14679797 ~ 14682980 (-)
G155770 LOC103376870 other downstream 1035224 14509233 ~ 14509614 (-)
G156206 klhl26,LOC107680559,LOC107597147 other upstream 394727 15954076 ~ 15957090 (-)
AMCG00006083 NA other upstream 894935 16454284 ~ 16462165 (-)
AMCG00006118 NA other upstream 946015 16505364 ~ 16521689 (-)
G156341 NA other upstream 1092191 16651540 ~ 16680772 (-)
AMCG00006127 NA other upstream 1388648 16947997 ~ 16963650 (-)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000075_00059491_00078552 UPF1, UPF1.S coding CI01000075 null 59491 ~ 78552 (-)