Gene loci information

Transcript annotation

  • This transcript has been annotated as Aryl hydrocarbon receptor nuclear translocator-like protein 1.

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.t2 isoform g5524.t2 10081511 10086705
chr_2 g5524 g5524.t2 exon g5524.t2.exon1 10081511 10081767
chr_2 g5524 g5524.t2 TTS g5524.t2 10081524 10081524
chr_2 g5524 g5524.t2 exon g5524.t2.exon2 10081943 10082784
chr_2 g5524 g5524.t2 cds g5524.t2.CDS1 10082741 10082784
chr_2 g5524 g5524.t2 exon g5524.t2.exon3 10082846 10082932
chr_2 g5524 g5524.t2 cds g5524.t2.CDS2 10082846 10082932
chr_2 g5524 g5524.t2 exon g5524.t2.exon4 10082982 10083287
chr_2 g5524 g5524.t2 cds g5524.t2.CDS3 10082982 10083287
chr_2 g5524 g5524.t2 exon g5524.t2.exon5 10083356 10083473
chr_2 g5524 g5524.t2 cds g5524.t2.CDS4 10083356 10083473
chr_2 g5524 g5524.t2 exon g5524.t2.exon6 10083533 10084209
chr_2 g5524 g5524.t2 cds g5524.t2.CDS5 10083533 10084209
chr_2 g5524 g5524.t2 exon g5524.t2.exon7 10084272 10084343
chr_2 g5524 g5524.t2 cds g5524.t2.CDS6 10084272 10084343
chr_2 g5524 g5524.t2 exon g5524.t2.exon8 10084407 10084501
chr_2 g5524 g5524.t2 cds g5524.t2.CDS7 10084407 10084501
chr_2 g5524 g5524.t2 exon g5524.t2.exon9 10084555 10084833
chr_2 g5524 g5524.t2 cds g5524.t2.CDS8 10084555 10084833
chr_2 g5524 g5524.t2 exon g5524.t2.exon10 10084940 10085005
chr_2 g5524 g5524.t2 cds g5524.t2.CDS9 10084940 10085005
chr_2 g5524 g5524.t2 exon g5524.t2.exon11 10086217 10086372
chr_2 g5524 g5524.t2 cds g5524.t2.CDS10 10086217 10086372
chr_2 g5524 g5524.t2 exon g5524.t2.exon12 10086442 10086634
chr_2 g5524 g5524.t2 cds g5524.t2.CDS11 10086442 10086634
chr_2 g5524 g5524.t2 exon g5524.t2.exon13 10086702 10086705
chr_2 g5524 g5524.t2 cds g5524.t2.CDS12 10086702 10086705
chr_2 g5524 g5524.t2 TSS g5524.t2 10086782 10086782

Sequences

>g5524.t2 Gene=g5524 Length=3152
ATGGATTTATCTTATTCACGGTTATTGTCAGTGTCATCTGATGACGAAAAAGAATTTGTG
ACATTAGAAGATTTAAAGGCACATCAATTGACTGATTTGGAGCAGCGATCAAAAGATAAT
TTGAAATTAATTGAACAAAAAGAGGAGCACGATCAAAGTTTTAATGTGTATTATGATTTA
AATACACACAAGCCAAACAGTGTTAGTAATCTGTATCAAGATATGACAATTGACACAAGT
TTTTTACCTGAATCAGACATCGCACTAATGGACTCATCAAACTCAATAAATACTGAAAAT
CTTCAAAATCAGTACATTCAAAAAAGTTCAAGAAAGAGGAAATTTTCATTGTCTGAAGTA
AGTGAAGATATTGAGGACGATGACGCTAAATCGATTAAAACTACAGATGACAATAAAAAG
GCAAATCATTCAGAGATCGAAAAAAGGCGTAGAGATAAAATGAATAATTTCATCACCGAG
CTTTCATCAATGATCCCAATGTGCCATGCCATGTCAAGAAAGTTAGATAAATTGACGGTC
TTACGAATGGCTGTCCAACATTTGAAAACCATTAGAGGCACAACAAATTCCTTCACTGCA
GATTATAAGCCAGCATTTTTATCTGACCAAGAATTAAAAATGTTGATTCTACAAGCTGCT
GAAGGATTTTTATTCGTCGTTGGGTGCGATCGTGGCCGAATTTTATATGTGTCCGAGTCA
GTTTCGGAAGTATTAAATTATACACAAGGAGAACTTTTAGGCCAATCATGGTTTGACATT
CTTCATCCGAAAGACATTGCAAAAGTTAAAGAGCAACTAAGTTCATCAGATTTGAGTCCA
CGCGAACGTCTCATAGATGCTAAAACAATGTTACCAGTTAAACATTCCGATGTCTCAATA
GTGACACAAAACATTTTCCCTGGTGCAAGAAGATCATTTTTCTGTCGTATGAAATGTAAA
TCGTCTGTTCAAATAAAGGAAGAAATTGATTCAAACAATACAACATCAAATTGCCATCGA
CGAAATAAAAAGCAAATGGCGGACAAGAAATTTGTTACAATTCAGAGCATTGGTTACTTA
AAGTCATGGGCACCTGCAAAAATTCTAGAAACATCTGAACAAGAATCTGAAGAGGGAGAC
TGTCTGTCTTTATCATGCCTTGTAGCTGTGGGAAGATTAGTAGATTACAACAATGACGGA
AGCTTTCAGAACATAAAAACTACAATTTCAAATAATGCAAAACGAGGAAATCCATCATTG
AGAAATGTTCATTTCATTTCACGACATGCAAATGATGGGAAATTTTTATTTGTTGATCAA
AGAGCTACATTAGTGTTAGGATTTCTTCCACAGGAACTTCTTGGTACAAGTATGTATGAA
TATTTTAATCATCGTGATATCGCTGCACTTGCTGACTCTCATAAAGTTGCATTGACGACA
ACAGAAAAAGTTACCACACCAATTTATGGTATGAGAACAAAAGATAATGGTTTTATCAAT
ATTCAAAGTGAATGGAAGTCATTTAAGAATCCATGGACTAGGGATATTGAATTTTTAATT
GCAAAAAATAATGTTATCTTTTCTGATTTGCGAAATTATGAAAATGGAAATCAAATTCGC
AATAATGGTAACGAAAGCAGTTATGACTTTTTGAATCAAACAAATGGTCGTGAAATGACG
AGAATGATTAATGTTCATATCGAGGCAAGTAAAATTGGACGACAAATTGCTGAGCAAGTG
CTTGACTATCAAAGACGTATGGGTGATGATGCTTCACCAGATTCAAGTAGTTCCGATCCT
GATCCAACACTTGCTATGTCATTAGCAGATGAAGGAAATCATCTTGCTTCCATGAATGTA
GAAAATAACAGTAATTCTGCTGCATCTAATGATATGCCTACTCGAATCAATGGCACATAT
TCAAACTTTGCAACATTCAATCATGATAGATCAAGTGTTGAAAATGGGACAAATGAAGTA
ACAACTGGTGATGGAAATGATGATGCATCAATGGCTGTATTAATGAATTTATTAGAAGCT
GATGCTGGTTTAGGTGGACCAATTGATTTTACAGGACTGCCATGGCCTCTTCCGTAATTG
AAGATGTAATCGAATCACATATAACCATCATTTGGTATAACTTTCTCATAAAACAAAGCT
GAAAGTTTAAACTTTTATTAATTAAATAAGGCAGCATTTTTGTTCCGAAAATATATTATA
TTTCCTATTAATTTCCAGTTAAATATTTTTTTTGAACATCTATTTAAATCATTAAGTATT
TAAAATCAGCATATCATTTTTCAATATTACTTCATCATCTGTTTTTGTCTTGTTGTAAAT
TGAACACTTTTACATACCATATTTCTTGTTTATTGTATCTACAGAATATTTTTAACAATT
TTTCGTCTCTTCATAATCTGTGAGTGTTTTTATGATCAAATATATGGGCTTCTCTGTGTA
TATTTATGTGCAAAGTGACAATTCCAAATTCATTTTAAACTTTATAAATTTTTAACAGCA
ACTCACGGCATAACTGACGCCTTTCACTATATCATTCTCTTTTATCTTTTTTTTATTATA
AAAATATTCTTTAAAATTTTAAAGTGTTTTTGTACTTTTAGATGAACACAAAATCATAAT
GATGAAATCTATCCTAAATGTCCAGTCACAGTGAGAAACTAAAGAAATGACAGCACGAAA
AGCATACAACAATTTTCTATCCTAAATTATACCATTCTTATTGCTGTCAAAAATCTATTG
GTCCTCTCACAAATGCTTTTCGTGATTGTCTAAAAAAATCATAATAAAAGTAAGAGAAAT
AACTTCATAGAGAAAACAAACAAGGGTTCGAACTTTTTTGCATATTTTACTTGATATTCT
CATATTTCTTGTCAATGACAAAAATATGCTAGTATCAAGCAAGTCCGAAACCTAACACAA
ACACACAAATAAAACTCTTAAATTTCCCTGCAAACATCCTATTGTTCTCCCTATAAAATT
CTCTTTTTTTGAAAAACTATAAAAGAAATAATAAGAATGTATGAATGGGCTAAAATAAAA
TTTTGAGTGTATAAAAAAATATAGAAATAATAAAAATAAATTTTTCAAATTTTATTCTTG
TCATTAATAAAACTGAACATTTCTCAAATTAA

>g5524.t2 Gene=g5524 Length=698
MDLSYSRLLSVSSDDEKEFVTLEDLKAHQLTDLEQRSKDNLKLIEQKEEHDQSFNVYYDL
NTHKPNSVSNLYQDMTIDTSFLPESDIALMDSSNSINTENLQNQYIQKSSRKRKFSLSEV
SEDIEDDDAKSIKTTDDNKKANHSEIEKRRRDKMNNFITELSSMIPMCHAMSRKLDKLTV
LRMAVQHLKTIRGTTNSFTADYKPAFLSDQELKMLILQAAEGFLFVVGCDRGRILYVSES
VSEVLNYTQGELLGQSWFDILHPKDIAKVKEQLSSSDLSPRERLIDAKTMLPVKHSDVSI
VTQNIFPGARRSFFCRMKCKSSVQIKEEIDSNNTTSNCHRRNKKQMADKKFVTIQSIGYL
KSWAPAKILETSEQESEEGDCLSLSCLVAVGRLVDYNNDGSFQNIKTTISNNAKRGNPSL
RNVHFISRHANDGKFLFVDQRATLVLGFLPQELLGTSMYEYFNHRDIAALADSHKVALTT
TEKVTTPIYGMRTKDNGFINIQSEWKSFKNPWTRDIEFLIAKNNVIFSDLRNYENGNQIR
NNGNESSYDFLNQTNGREMTRMINVHIEASKIGRQIAEQVLDYQRRMGDDASPDSSSSDP
DPTLAMSLADEGNHLASMNVENNSNSAASNDMPTRINGTYSNFATFNHDRSSVENGTNEV
TTGDGNDDASMAVLMNLLEADAGLGGPIDFTGLPWPLP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g5524.t2 CDD cd00130 PAS 222 276 0.0000000
20 g5524.t2 CDD cd00130 PAS 425 520 0.0000000
17 g5524.t2 Gene3D G3DSA:4.10.280.10 HLH 129 194 0.0000000
19 g5524.t2 Gene3D G3DSA:3.30.450.20 - 200 397 0.0000000
18 g5524.t2 Gene3D G3DSA:3.30.450.20 - 415 568 0.0000000
4 g5524.t2 PANTHER PTHR23042 CIRCADIAN PROTEIN CLOCK/ARNT/BMAL/PAS 116 698 0.0000000
5 g5524.t2 PANTHER PTHR23042:SF99 PROTEIN CYCLE 116 698 0.0000000
12 g5524.t2 PRINTS PR00785 Nuclear translocator signature 153 168 0.0000000
13 g5524.t2 PRINTS PR00785 Nuclear translocator signature 173 193 0.0000000
10 g5524.t2 PRINTS PR00785 Nuclear translocator signature 202 225 0.0000000
9 g5524.t2 PRINTS PR00785 Nuclear translocator signature 227 246 0.0000000
7 g5524.t2 PRINTS PR00785 Nuclear translocator signature 259 277 0.0000000
11 g5524.t2 PRINTS PR00785 Nuclear translocator signature 307 320 0.0000000
6 g5524.t2 PRINTS PR00785 Nuclear translocator signature 351 370 0.0000000
8 g5524.t2 PRINTS PR00785 Nuclear translocator signature 385 401 0.0000000
1 g5524.t2 Pfam PF00010 Helix-loop-helix DNA-binding domain 139 190 0.0000000
3 g5524.t2 Pfam PF08447 PAS fold 234 273 0.0000011
2 g5524.t2 Pfam PF14598 PAS domain 425 526 0.0000000
26 g5524.t2 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 138 191 16.6090000
27 g5524.t2 ProSiteProfiles PS50112 PAS repeat profile. 209 273 15.0610000
28 g5524.t2 ProSiteProfiles PS50112 PAS repeat profile. 432 481 10.7470000
22 g5524.t2 SMART SM00353 finulus 144 197 0.0000000
24 g5524.t2 SMART SM00091 pas_2 211 278 0.0000000
23 g5524.t2 SMART SM00091 pas_2 413 479 0.0002700
16 g5524.t2 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 137 220 0.0000000
15 g5524.t2 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 221 322 0.0000000
14 g5524.t2 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 425 524 0.0000000
25 g5524.t2 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 230 275 0.0000084

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5524/g5524.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5524.t2.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

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