Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein cycle.

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 g5524 g5524.t4 isoform g5524.t4 10083533 10086705
chr_2 g5524 g5524.t4 exon g5524.t4.exon1 10083533 10084209
chr_2 g5524 g5524.t4 cds g5524.t4.CDS1 10083533 10084209
chr_2 g5524 g5524.t4 exon g5524.t4.exon2 10084272 10084343
chr_2 g5524 g5524.t4 cds g5524.t4.CDS2 10084272 10084343
chr_2 g5524 g5524.t4 exon g5524.t4.exon3 10084407 10084501
chr_2 g5524 g5524.t4 cds g5524.t4.CDS3 10084407 10084501
chr_2 g5524 g5524.t4 exon g5524.t4.exon4 10084555 10084770
chr_2 g5524 g5524.t4 cds g5524.t4.CDS4 10084555 10084770
chr_2 g5524 g5524.t4 exon g5524.t4.exon5 10086217 10086372
chr_2 g5524 g5524.t4 cds g5524.t4.CDS5 10086217 10086372
chr_2 g5524 g5524.t4 exon g5524.t4.exon6 10086442 10086634
chr_2 g5524 g5524.t4 cds g5524.t4.CDS6 10086442 10086634
chr_2 g5524 g5524.t4 exon g5524.t4.exon7 10086702 10086705
chr_2 g5524 g5524.t4 cds g5524.t4.CDS7 10086702 10086705
chr_2 g5524 g5524.t4 TSS g5524.t4 10086782 10086782
chr_2 g5524 g5524.t4 TTS g5524.t4 NA NA

Sequences

>g5524.t4 Gene=g5524 Length=1413
ATGGATTTATCTTATTCACGGTTATTGTCAGTGTCATCTGATGACGAAAAAGAATTTGTG
ACATTAGAAGATTTAAAGGCACATCAATTGACTGATTTGGAGCAGCGATCAAAAGATAAT
TTGAAATTAATTGAACAAAAAGAGGAGCACGATCAAAGTTTTAATGTGTATTATGATTTA
AATACACACAAGCCAAACAGTGTTAGTAATCTGTATCAAGATATGACAATTGACACAAGT
TTTTTACCTGAATCAGACATCGCACTAATGGACTCATCAAACTCAATAAATACTGAAAAT
CTTCAAAATCAGTACATTCAAAAAAGTTCAAGAAAGAGGAAATTTTCATTGTCTTCATCA
ATGATCCCAATGTGCCATGCCATGTCAAGAAAGTTAGATAAATTGACGGTCTTACGAATG
GCTGTCCAACATTTGAAAACCATTAGAGGCACAACAAATTCCTTCACTGCAGATTATAAG
CCAGCATTTTTATCTGACCAAGAATTAAAAATGTTGATTCTACAAGCTGCTGAAGGATTT
TTATTCGTCGTTGGGTGCGATCGTGGCCGAATTTTATATGTGTCCGAGTCAGTTTCGGAA
GTATTAAATTATACACAAGGAGAACTTTTAGGCCAATCATGGTTTGACATTCTTCATCCG
AAAGACATTGCAAAAGTTAAAGAGCAACTAAGTTCATCAGATTTGAGTCCACGCGAACGT
CTCATAGATGCTAAAACAATGTTACCAGTTAAACATTCCGATGTCTCAATAGTGACACAA
AACATTTTCCCTGGTGCAAGAAGATCATTTTTCTGTCGTATGAAATGTAAATCGTCTGTT
CAAATAAAGGAAGAAATTGATTCAAACAATACAACATCAAATTGCCATCGACGAAATAAA
AAGCAAATGGCGGACAAGAAATTTGTTACAATTCAGAGCATTGGTTACTTAAAGTCATGG
GCACCTGCAAAAATTCTAGAAACATCTGAACAAGAATCTGAAGAGGGAGACTGTCTGTCT
TTATCATGCCTTGTAGCTGTGGGAAGATTAGTAGATTACAACAATGACGGAAGCTTTCAG
AACATAAAAACTACAATTTCAAATAATGCAAAACGAGGAAATCCATCATTGAGAAATGTT
CATTTCATTTCACGACATGCAAATGATGGGAAATTTTTATTTGTTGATCAAAGAGCTACA
TTAGTGTTAGGATTTCTTCCACAGGAACTTCTTGGTACAAGTATGTATGAATATTTTAAT
CATCGTGATATCGCTGCACTTGCTGACTCTCATAAAGTTGCATTGACGACAACAGAAAAA
GTTACCACACCAATTTATGGTATGAGAACAAAAGATAATGGTTTTATCAATATTCAAAGT
GAATGGAAGTCATTTAAGAATCCATGGACTAGG

>g5524.t4 Gene=g5524 Length=471
MDLSYSRLLSVSSDDEKEFVTLEDLKAHQLTDLEQRSKDNLKLIEQKEEHDQSFNVYYDL
NTHKPNSVSNLYQDMTIDTSFLPESDIALMDSSNSINTENLQNQYIQKSSRKRKFSLSSS
MIPMCHAMSRKLDKLTVLRMAVQHLKTIRGTTNSFTADYKPAFLSDQELKMLILQAAEGF
LFVVGCDRGRILYVSESVSEVLNYTQGELLGQSWFDILHPKDIAKVKEQLSSSDLSPRER
LIDAKTMLPVKHSDVSIVTQNIFPGARRSFFCRMKCKSSVQIKEEIDSNNTTSNCHRRNK
KQMADKKFVTIQSIGYLKSWAPAKILETSEQESEEGDCLSLSCLVAVGRLVDYNNDGSFQ
NIKTTISNNAKRGNPSLRNVHFISRHANDGKFLFVDQRATLVLGFLPQELLGTSMYEYFN
HRDIAALADSHKVALTTTEKVTTPIYGMRTKDNGFINIQSEWKSFKNPWTR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g5524.t4 CDD cd00130 PAS 179 243 0.0000000
20 g5524.t4 CDD cd00130 PAS 382 471 0.0000000
16 g5524.t4 Gene3D G3DSA:4.10.280.10 HLH 111 157 0.0000031
17 g5524.t4 Gene3D G3DSA:3.30.450.20 - 158 354 0.0000000
18 g5524.t4 Gene3D G3DSA:3.30.450.20 - 372 471 0.0000000
3 g5524.t4 PANTHER PTHR23042 CIRCADIAN PROTEIN CLOCK/ARNT/BMAL/PAS 119 470 0.0000000
4 g5524.t4 PANTHER PTHR23042:SF99 PROTEIN CYCLE 119 470 0.0000000
11 g5524.t4 PRINTS PR00785 Nuclear translocator signature 110 125 0.0000000
10 g5524.t4 PRINTS PR00785 Nuclear translocator signature 130 150 0.0000000
5 g5524.t4 PRINTS PR00785 Nuclear translocator signature 159 182 0.0000000
12 g5524.t4 PRINTS PR00785 Nuclear translocator signature 184 203 0.0000000
9 g5524.t4 PRINTS PR00785 Nuclear translocator signature 216 234 0.0000000
8 g5524.t4 PRINTS PR00785 Nuclear translocator signature 264 277 0.0000000
7 g5524.t4 PRINTS PR00785 Nuclear translocator signature 308 327 0.0000000
6 g5524.t4 PRINTS PR00785 Nuclear translocator signature 342 358 0.0000000
2 g5524.t4 Pfam PF08447 PAS fold 191 230 0.0000007
1 g5524.t4 Pfam PF14598 PAS domain 382 470 0.0000000
24 g5524.t4 ProSiteProfiles PS50112 PAS repeat profile. 166 230 15.0610000
25 g5524.t4 ProSiteProfiles PS50112 PAS repeat profile. 389 438 10.7470000
22 g5524.t4 SMART SM00091 pas_2 168 235 0.0000000
21 g5524.t4 SMART SM00091 pas_2 370 436 0.0002700
15 g5524.t4 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 119 178 0.0000432
14 g5524.t4 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 178 279 0.0000000
13 g5524.t4 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 382 470 0.0000000
23 g5524.t4 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 187 232 0.0000047

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5524/g5524.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5524.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005634 nucleus CC
GO:0005515 protein binding MF
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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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