Gene loci information

Transcript annotation

  • This transcript has been annotated as Circadian locomoter output cycles protein kaput.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_2 g7121 g7121.t1 isoform g7121.t1 21339919 21342769
chr_2 g7121 g7121.t1 exon g7121.t1.exon1 21339919 21340105
chr_2 g7121 g7121.t1 cds g7121.t1.CDS1 21339919 21340105
chr_2 g7121 g7121.t1 exon g7121.t1.exon2 21340167 21340348
chr_2 g7121 g7121.t1 cds g7121.t1.CDS2 21340167 21340348
chr_2 g7121 g7121.t1 exon g7121.t1.exon3 21340421 21340637
chr_2 g7121 g7121.t1 cds g7121.t1.CDS3 21340421 21340637
chr_2 g7121 g7121.t1 exon g7121.t1.exon4 21340701 21341006
chr_2 g7121 g7121.t1 cds g7121.t1.CDS4 21340701 21341006
chr_2 g7121 g7121.t1 exon g7121.t1.exon5 21341079 21341533
chr_2 g7121 g7121.t1 cds g7121.t1.CDS5 21341079 21341533
chr_2 g7121 g7121.t1 exon g7121.t1.exon6 21341603 21342769
chr_2 g7121 g7121.t1 cds g7121.t1.CDS6 21341603 21342769
chr_2 g7121 g7121.t1 TTS g7121.t1 21343204 21343204
chr_2 g7121 g7121.t1 TSS g7121.t1 NA NA

Sequences

>g7121.t1 Gene=g7121 Length=2514
ATGATGGACGACGATGATGACAAGGATGACAGCAAGAGGAAATCACGTAATCTTAGTGAA
AAGAAAAGGCGCGATCAATTTAATTTATTAGTTAATGAACTAAGTTCAATGGTATCAACA
AATAGTAGAAAAATGGATAAATCAACAGTCTTAAAAACAACTATTGCATTTTTGAAAAAT
CATAATGAAATCTCAGTGAGATCTCGAGCGCATGAAATTCAGGAAAACTGGAAGCCATCA
TTTCTGCCGAATGAAGAATTTTCGCATCTGATACTCGAAGCTTTGGATGGCTTCATAATT
GTGTTCTCATCCACTGGAAAAATTTATTATACATCTGAAAGCATTACATCACTTCTCTCC
CATTTACCCAGTGATCTACTGAATATGACAATTTATGATTTGGTTTATGAGGAGGAGCAG
CAAGACATATATAATTTGCTTTTAAATCCACCTAAATCAGTTGATCCAATGCAGAGTGGG
ATTAATTCAGAGAATCAGGTTTCATTTACTTGTCACGTTAAGCGTGGATCTCTCGATAAC
TCATCTCCATTATCATATGAATATGTACAGTTTAATGGATATTTTAGAGATAACATAGAT
GTAGATAGTATGATGCCATCGAGATATAGTGGTTATTCTGGTGAAGCCGATACGAGACTA
ATATTTGTTGGAACTGGTCGTTTACTCACACCCCAACTCATAAGAGAAATGTCAATAGTT
GACACAAAAAGCGAATTCACATCTCGACATAGTCTTGAATGGAAATTTCTTTTTCTAGAT
CATCGAGCTTCACAAATTATTGGTTATTTACCTTTTGAAGTACTTGGAACATCAGGTTAT
GACTATTACCATTTTGATGACCTTGAACGAGTTGTCACGTGTCATGAGGCATTAATGCAA
AAAGGAGAAGGGACATCATGTTATTATCGATTTTTAACGAAAGGACAACAGTGGATATGG
TTGCAAACACGTTTTTATATAACTTATCATCAATGGAATTCAAAACCAGAATTTGTTGTG
TGCACACATAGAGTTGTAAGCTATGCTGATGTCATGAAACAAATGAGAAAAAGTGGAAAT
GGAACTGCTTTAAAGGACATTGATGATAATGATAGTGCAACTGAGGATCGTGGTAAAGCG
CCAACTTCAACTTCAATGATGGCCACTTCACCTTGGAGTTCAAAAAGTTCAAGAGCATCT
AAATCAATTGCACATACTCAAGAATCTCCTAATATTAAAATGAAACGGTATCAATCATAT
CGACCAGATTCTGATTCGACTTCAATGTCTGCTGATTCACCACTCAGTCATCATTCAATT
TTGACACAACATAGTTCAGTTAGTCAGCGTTCAAGATCTCGTCCAAATGTACAAATGCCA
AAATTATCAAATCAACAACATCAACAGTTGCATCAATCCCATCAATTACATACGCAGCAT
CATCAGCAATATTCGCAGTTTAATTTACCTCATCCTCAAATACATTCATCGAATACGCAG
CAACAACAGTCGTCTCAGACGATGAATCAATCGCAGCAGCAAGGAATGACAATTCACCCG
CCTCCATTGACCAGTCAAATTATGCCACATCATCATCAACGGACATCTGCACCAGCGCAA
ATTATTGGTACTCCATTTATTGATCAATCACAATATTTGACAGCTATTCCTGTGCAACCA
GTAATTGCGACACCAACTTCTTTCCCCGCCTCAGCAACTGTGATCTCACCTCTCCTTCCA
CCACCCGATTATGTTCATTCAAACGTAGTCTTAACTCCCGCACAAAATCAAATACAAGAT
CATTTGCAAAGAAAACATGAAGAGTTGCAGAAACTCATTGTGCAACAACAAGATGAATTA
AGGCGAGTAAGTGAACAATTATTTATGGCTCGTTATGGGCTTCTTCCACCTATTGTGAAT
GTTTCATTACCATTTGTTGCTCCTATGGAACACTCCTCTGATACTGGTGAAAATAGTAGA
TGTATGAGTACAACTTCTTCACATTTATCTCAACAACAACAACCTTATGAACAGCAACAA
CAAATGATTCAAATGTCGTCAACACAGAATCAGTCAAGCACACAAGTTCATGTGCAACAA
CATTCAATGACTCAGCAACAAAATCAGACGCCACAAGTTATGCATCATAATATTATCCAG
CAACAACAACAGCAATCTAATCAACAGCAGCAGCAACAACAACAACAGAGTCATATGACT
GTAACATATGAAATGAATCCAACACAAAAAACAAATATATCGACACATATCGATCAATCG
ATGGAAGCTGATCAAACAAATAATGATATAATGCAATATATGCAACACCAAGCGCATAGC
ATTAGTAATCAAAATAATCAGACAGGAGGCATTCACCAATTGTCACAACAACAACAACAG
CAGATGATGACTAATGATGAGTTTGAGTTGATTCCTTTTCAAATGATGAATTCACAAATT
CTTTATTCCAGTGGAACAACAAATAGTACCAACAATAATGCTAACAACAAATGA

>g7121.t1 Gene=g7121 Length=837
MMDDDDDKDDSKRKSRNLSEKKRRDQFNLLVNELSSMVSTNSRKMDKSTVLKTTIAFLKN
HNEISVRSRAHEIQENWKPSFLPNEEFSHLILEALDGFIIVFSSTGKIYYTSESITSLLS
HLPSDLLNMTIYDLVYEEEQQDIYNLLLNPPKSVDPMQSGINSENQVSFTCHVKRGSLDN
SSPLSYEYVQFNGYFRDNIDVDSMMPSRYSGYSGEADTRLIFVGTGRLLTPQLIREMSIV
DTKSEFTSRHSLEWKFLFLDHRASQIIGYLPFEVLGTSGYDYYHFDDLERVVTCHEALMQ
KGEGTSCYYRFLTKGQQWIWLQTRFYITYHQWNSKPEFVVCTHRVVSYADVMKQMRKSGN
GTALKDIDDNDSATEDRGKAPTSTSMMATSPWSSKSSRASKSIAHTQESPNIKMKRYQSY
RPDSDSTSMSADSPLSHHSILTQHSSVSQRSRSRPNVQMPKLSNQQHQQLHQSHQLHTQH
HQQYSQFNLPHPQIHSSNTQQQQSSQTMNQSQQQGMTIHPPPLTSQIMPHHHQRTSAPAQ
IIGTPFIDQSQYLTAIPVQPVIATPTSFPASATVISPLLPPPDYVHSNVVLTPAQNQIQD
HLQRKHEELQKLIVQQQDELRRVSEQLFMARYGLLPPIVNVSLPFVAPMEHSSDTGENSR
CMSTTSSHLSQQQQPYEQQQQMIQMSSTQNQSSTQVHVQQHSMTQQQNQTPQVMHHNIIQ
QQQQQSNQQQQQQQQQSHMTVTYEMNPTQKTNISTHIDQSMEADQTNNDIMQYMQHQAHS
ISNQNNQTGGIHQLSQQQQQQMMTNDEFELIPFQMMNSQILYSSGTTNSTNNNANNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g7121.t1 CDD cd00130 PAS 95 149 1.52457E-5
19 g7121.t1 CDD cd00130 PAS 244 345 2.44145E-17
17 g7121.t1 Coils Coil Coil 599 626 -
14 g7121.t1 Gene3D G3DSA:4.10.280.10 HLH 19 95 8.1E-24
16 g7121.t1 Gene3D G3DSA:3.30.450.20 - 96 233 5.8E-34
15 g7121.t1 Gene3D G3DSA:3.30.450.20 - 235 353 1.3E-38
27 g7121.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 21 -
24 g7121.t1 MobiDBLite mobidb-lite consensus disorder prediction 362 376 -
28 g7121.t1 MobiDBLite mobidb-lite consensus disorder prediction 362 516 -
26 g7121.t1 MobiDBLite mobidb-lite consensus disorder prediction 377 414 -
25 g7121.t1 MobiDBLite mobidb-lite consensus disorder prediction 421 516 -
29 g7121.t1 MobiDBLite mobidb-lite consensus disorder prediction 654 739 -
4 g7121.t1 PANTHER PTHR46055 CIRCADIAN LOCOMOTER OUTPUT CYCLES PROTEIN KAPUT 1 402 1.1E-239
6 g7121.t1 PANTHER PTHR46055:SF3 CIRCADIAN LOCOMOTER OUTPUT CYCLES PROTEIN KAPUT 1 402 1.1E-239
5 g7121.t1 PANTHER PTHR46055 CIRCADIAN LOCOMOTER OUTPUT CYCLES PROTEIN KAPUT 393 756 1.1E-239
7 g7121.t1 PANTHER PTHR46055:SF3 CIRCADIAN LOCOMOTER OUTPUT CYCLES PROTEIN KAPUT 393 756 1.1E-239
8 g7121.t1 PRINTS PR00785 Nuclear translocator signature 26 41 7.1E-15
10 g7121.t1 PRINTS PR00785 Nuclear translocator signature 77 100 7.1E-15
9 g7121.t1 PRINTS PR00785 Nuclear translocator signature 245 262 7.1E-15
2 g7121.t1 Pfam PF00010 Helix-loop-helix DNA-binding domain 12 60 4.4E-7
1 g7121.t1 Pfam PF00989 PAS fold 90 146 1.5E-5
3 g7121.t1 Pfam PF14598 PAS domain 244 347 3.1E-19
30 g7121.t1 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 11 61 13.548
31 g7121.t1 ProSiteProfiles PS50112 PAS repeat profile. 84 147 12.164
32 g7121.t1 ProSiteProfiles PS50112 PAS repeat profile. 255 302 9.749
20 g7121.t1 SMART SM00353 finulus 17 67 2.1E-6
21 g7121.t1 SMART SM00091 pas_2 86 152 1.1E-6
22 g7121.t1 SMART SM00091 pas_2 234 300 6.4E-8
23 g7121.t1 SMART SM00086 pac_2 306 349 8.9E-7
13 g7121.t1 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 8 66 2.49E-11
12 g7121.t1 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 95 141 4.97E-7
11 g7121.t1 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 245 346 4.19E-24

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005634 nucleus CC
GO:0006355 regulation of transcription, DNA-templated BP
GO:0005667 transcription regulator complex CC
GO:0005737 cytoplasm CC
GO:0003700 DNA-binding transcription factor activity MF
GO:0046983 protein dimerization activity MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values