RNA id: XM_034313929.1


Basic Information

Item Value
RNA id XM_034313929.1
length 4017
RNA type mRNA
GC content 0.52
exon number 23
gene id clocka
representative True

Chromosome Information

Item Value
chromosome id NC_047613.1
NCBI id CM018559.1
chromosome length 22090854
location 4248330 ~ 4309929 (+)
genome version GENO_Phyp_1.0_2019_striped_catfish_Genome
species striped catfish
(Pangasianodon hypophthalmus)

Sequence

atgttagAGTATGTGTCCTTTAAAATGAAACAGGAGACTGACTGCGCCgctaaagttgttttttttcccgtattgtttaaataaaagctaGTTTGTCGTTTGACACGACGTTAAAATATCCTCCTCGCGCTACAatgtagcctgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttgccagaTTGTGTAGGCTGCTTCTGCTGCTGCCGCTTAGTGTgcagtgcgcatgcgcgtgGGAAGCCCAGGGTAGGCCCTGCTGTTTTTGTAACTCCAGTCAATCCAACGCAGGCGTCTGAACCAAAACAAGGAGCGCGAGATCCCCTCATGACGGCGAATAAACTGGGTGACAACACTAATCTGAGGACCTAGGCAAAAAGGAATCATTTCTGAAGTCATGACCTAAGACGAGTTTGCTGCTGACATGCGGTACATGTGCGCTCACCCTCCTTGGAAAACATTCAGATGCTACAGGGACCCACAGCACACTTGTGATCATTTTAAACCACAGCCTCTCTCCGATTTCTCAAAGCTCTCCTTACTACACGTGAAAAACTGACGCAAATCCACACTGACTCACAGCCCAAGTGGATTGTGGTGGACTTCATCCTGAGACGAGCTCCTCATTCTCACTTTGCGCGCAGGACTGGAGGTTGGTTTGGCTTCAAAATGAAACCGAGGCCACGTTCAGACCTGGTATCAACACCTGTCTCAGGTGATCTGGCGATCTGATTACAGGTGGACAGCTGAGACGGATAGCCATTAACACCTATTTTCATGCATCTTGAACGCTTCTCCAGTGATCATTTGTGATTGTTCTTCTTGAATAACATAGCTGACCAGGAGGTTCTTTAAAGTTATCAGTGAGGTTCATGTACAAATGTCTACCTCACGCTTAAAGCTCCTCTGTGTCCCACTGCAGCCCTGATCACATttcaaaatgacctccagcataGACCGgGATGACAGCAGTATCTTTGATGGACTGATGGAAGAAGATGAGAAGGACAAAGCAAAACGAGTTTCCAGGAACAAGTCGGAAAAGAAGAGGCGAGACCAGTTCAATGTGCTCATCAAGGAGCTGGGCACCATGCTGCCTGGCAACACCCGCAAGATGGACAAATCCACCATTCTGCAGAAAAGCATTGACTTCCTGCGCAAGCACAAAGAAATTGCAGCACAGTCGGAGTCCAGTGAGATTCGTCAGGACTGGAAGCCTCCGTTCCTCAGCAACGAGGAGTTTACACAGCTGATGTTAGAGGCCCTAGATGGCTTCTTTCTAGCCATTATGACAGACGGCAACATAATCTACGTGTCTGAAAGTGTCACCTCTTTACTAGAGCATTTACCAtctgaCCTGGTGGACCAGAACCTGTTGAATTTTCTTCCACTGGGAGAGCACTCTGAAGTGTACAAAGCCCTCTCAACACACATACTCGAAGGAGAGAGCCTCACACCAGACCACTTAAAGACAAAAAACCAGTTAGAGTTCTGCTGCCACATGCTCCGGGGCACCATCGACCCCAAAGAGCCTCCCGTCTACGAGTATGTAAAGTTTATCGGAAACTTCAAGTCTCTCAACACTGTGCCTAACTCGACACGGAACGGCTTTGAAGGTGTGATCCAGCGCTCGCTCAGGCCCTCGTTTGAAGACCGCGTGTGTTTCATTGCCACTGTGAGGTTAGCCAAGCCTCAGTTTATCAAGGAGATGTGCACTGTGGAGGAACCCAATGAGGAGTTCACTTCCAGACACAGCTTAGAGTGGAAATTCCTTTTCCTGGAccacagGGCGCCCCCTATCATAGGTTACCTGCCTTTCGAAGTTTTGGGCACATCGGGGTATGATTACTATCACGTAGATGACTTGGAGACCCTTGCCAAGTGCCATGAACACCtGATGCAGTATGGGAAAGGGAAGTCGTGCTATTATCGGTTCTTGACCAAAGGCCAGCAGTGGATTTGGCTGCAGACTCACTACTACATCACCTACCACCAGTGGAACTCGCGGCCTGAGTTCAttgtctgcacacacactgttgtcAGCTATGCTGAGGTTAGGGCTGAGCAGCGCAGAGAGCTGGGCATCGAGGAGTCACCTCCTGAGATCTCTGCAGACAAGTCTCAAGACTCGGGCTCTGAGTCTCAGTTGAACACCTCCAGCCTGAAGGAGGCACTGGAGCGCTTTGATCAGAGTCGCACGCCCTCAGCCTCCTCCCGGAGCTCACGGAAGTCCTCCTCACACACCGCCGTTTCCGACCCCACCTccACCCAGACAAAGCTACAGACAGAGCACAGTACGCCGCCCCGCCAATCTGTCTCTACTATTGAAAAGACTTCTCAGCGCCGATCATCCATCAGcagccagTCGATGAGCTCTCAGAATACGAGCCAGACGATGGCAGCTTGTCTGGTGTCTCAGCCTCAGCAGCCACAGCAGCTGCAGCCTACtgtgcagccAGTGCTACAGTTCTCCACACAGCTGGATGCCATGCAGCACCTGAAGGAACAGCTGGAGCAGCGCACGCGTATGATCGAGGCTAACATCCAGAGGCAGCAAGAGGAGCTGCGTCAGATTCAGGAGGAGCTGCAAAGGGTGCAGGGCCAGGGCTTACAGatgttccTGCAGCAAGGTGGCGGTAGTCTGAACCTTGGCTCGGTGCAGTTAGCGCAGGGTTCCTCGGTGCAGCCAGGCACGGCTCTGACCATGCAGGGGCTGGTGGTGCCTGCAGGAATCTTACAAGGCAACCTGGCATCAACACATACGGGCACACAGCACTCTGTCACTCAGCAGACCCAGCCAGCTCAGCCTCAGCAGCAGAGCATTCTCCGAGAGCAgagtggcacacacacacagTCCCAGAGATCGTCGCACACACTGCAGTCTCCTCAGGGAGCCCTGCCTGCGTCTCTCTACAACACCATGATGATTTCACAGCCTGGTCAGGCCAACGTGGTGCAGATCTCCACCAGTTTAACCCAGAGCAGTCCGAGTGGAACCGCAGTCGCCACCTTCTCTCAGGACCGCCAGATACGATTCCCAGCAGCCCCTCAGCTCCTTACTAAGTTAGTGACGGGGCCTATGGCATGTGGCGCCGTCATGGTGCCCACCACCATGTTCATGGGTCAGGTGGTGACACCGTTTGCCCCTCAGCAGAGTCAAAATCAGACCATCAGCATTGGACAGCAAGCACCCACACCCTCGCAGGAGCAGCAGGGCCAGACGCAGGCCGGCACACAACCACAGAGCCAAAACCAGACTCCACTTAGCCAGACTCAGTTCCTCCAGGCACCTCGTCTTCTTCATGGGAATCAGTCAGCGCAGCTGATCCTCCAGGCAGCGTTTCCTCTCCAGCAGCAGAACGCCTTCGCCGCAACcacacaacagcagcagcaggtgcagcagcagcagctccaaCAGCAACATCAGCACCAACAGCAGCTtcagcatcagcagcagcagcagcagctggctTCTCATAGGCCAGACAGCATGTTGGACCGCTCCAATGCCCCGCCTCAGTAACCCGGCACCAGCCAATTGCGTGGCGAGGACCGAATCTGACCTCTGTTGTGCAGGGCGACGAAGGACGAGTATTTGCAGTATTCAAACTGTACCTGTTATTTGGCGCAAAGCAAAAGGTGCTGTTGTGTCTCTGCGCCCTACATGTCATCCCTCACCAAGTTCTGGATGCTTGCACTGAATTCTGGGAAGCATAGCCCACACTGGCTGAGTGGTTAGTAAGCTAGCAAGGGAGCccttggtttattttttaccaACCGAATCAAGATAAGAGGCAAGGCAAGTTGTGAGGTGGGCCGTctttcattcacacattcacatattaaTTTATGTAGAACGCTCCAGTTTGTGGACTGGAGGTGATTCAAGACTTCAGAGAAGTCCTGTAGGACAAATGGCACCACATCCATTTGTTCTTCTCCATTCATATCCTCCCTTCCCTGCTCTCTTCTTTTCATCTTTGTGTtttccatgtaaaaaaaaaaaaaaaaa

Function

GO:

id name namespace
GO:0009266 response to temperature stimulus biological_process
GO:0032922 circadian regulation of gene expression biological_process
GO:0009648 photoperiodism biological_process
GO:0045893 positive regulation of transcription, DNA-templated biological_process
GO:0007165 signal transduction biological_process
GO:0005634 nucleus cellular_component
GO:0005667 transcription regulator complex cellular_component
GO:0005737 cytoplasm cellular_component
GO:0003677 DNA binding molecular_function
GO:0004871 obsolete signal transducer activity molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0046982 protein heterodimerization activity molecular_function

KEGG:

id description
K02223 CLOCK, KAT13D; circadian locomoter output cycles kaput protein

JBrowse2

Neighbor

RNA id RNA type direction distance location representative gene id
XR_004580146.1 lncRNA upstream 4379 4239026 ~ 4243951 (+) True LOC117599777
TU342961 lncRNA upstream 174364 4061818 ~ 4073966 (+) True G289530
TU342957 lncRNA upstream 174364 4062764 ~ 4073966 (+) False G289530
TU342967 lncRNA upstream 177963 4054457 ~ 4070367 (+) True G289531
TU342965 lncRNA upstream 178615 4054457 ~ 4069715 (+) False G289531
TU343083 lncRNA downstream 9532 4319461 ~ 4330272 (+) True G289619
TU343090 lncRNA downstream 18919 4328848 ~ 4338299 (+) True trnad-guc_17
TU342943 lncRNA downstream 35650 4345579 ~ 4363088 (+) True G289521
XR_004580081.1 lncRNA downstream 40819 4350748 ~ 4352801 (+) True LOC117599675
TU343335 lncRNA downstream 123306 4433235 ~ 4434790 (+) True G289831
XM_034313840.1 mRNA upstream 9409 4235827 ~ 4238921 (+) True nmu
XM_034313506.1 mRNA upstream 51890 4176531 ~ 4196440 (+) False cep135
XM_034313504.1 mRNA upstream 51891 4176533 ~ 4196439 (+) True cep135
XM_026944620.2 mRNA upstream 51891 4176533 ~ 4196439 (+) False cep135
XM_026944619.2 mRNA upstream 51892 4176534 ~ 4196438 (+) False cep135
XM_026944622.2 mRNA downstream 56836 4366765 ~ 4396120 (+) True LOC113545323
XM_034313494.1 mRNA downstream 97839 4407768 ~ 4419833 (+) False LOC113545214
XM_026944426.2 mRNA downstream 97839 4407768 ~ 4419833 (+) False LOC113545214
XM_034313496.1 mRNA downstream 97839 4407768 ~ 4419833 (+) False LOC113545214
XM_034313495.1 mRNA downstream 98836 4408765 ~ 4419833 (+) True LOC113545214
TU342966 other upstream 178615 4063635 ~ 4069715 (+) False G289531
trnad-guc_14 other upstream 260207 3988052 ~ 3988123 (+) True trnad-guc_14
XR_004580118.1 other upstream 268545 3943495 ~ 3979785 (+) False ipo13
XR_003404754.1 other upstream 880558 3367648 ~ 3367772 (+) True LOC113546886
XR_003404755.1 other upstream 882928 3365278 ~ 3365402 (+) True LOC113546887
trnad-guc_16 other downstream 17542 4327471 ~ 4327542 (+) True trnad-guc_16
trnad-guc_17 other downstream 18903 4328832 ~ 4328903 (+) False trnad-guc_17
trnad-guc_18 other downstream 23629 4333558 ~ 4333629 (+) True trnad-guc_18
trnad-guc_19 other downstream 27974 4337903 ~ 4337974 (+) True trnad-guc_19
trnad-guc_22 other downstream 39879 4349808 ~ 4349879 (+) True trnad-guc_22

Expression Profile