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.t1 isoform g5524.t1 10082741 10086705
chr_2 g5524 g5524.t1 exon g5524.t1.exon1 10082741 10082784
chr_2 g5524 g5524.t1 cds g5524.t1.CDS1 10082741 10082784
chr_2 g5524 g5524.t1 exon g5524.t1.exon2 10082846 10082932
chr_2 g5524 g5524.t1 cds g5524.t1.CDS2 10082846 10082932
chr_2 g5524 g5524.t1 exon g5524.t1.exon3 10082982 10083287
chr_2 g5524 g5524.t1 cds g5524.t1.CDS3 10082982 10083287
chr_2 g5524 g5524.t1 exon g5524.t1.exon4 10083356 10083473
chr_2 g5524 g5524.t1 cds g5524.t1.CDS4 10083356 10083473
chr_2 g5524 g5524.t1 exon g5524.t1.exon5 10083533 10084209
chr_2 g5524 g5524.t1 cds g5524.t1.CDS5 10083533 10084209
chr_2 g5524 g5524.t1 exon g5524.t1.exon6 10084272 10084343
chr_2 g5524 g5524.t1 cds g5524.t1.CDS6 10084272 10084343
chr_2 g5524 g5524.t1 exon g5524.t1.exon7 10084407 10084501
chr_2 g5524 g5524.t1 cds g5524.t1.CDS7 10084407 10084501
chr_2 g5524 g5524.t1 exon g5524.t1.exon8 10084555 10084833
chr_2 g5524 g5524.t1 cds g5524.t1.CDS8 10084555 10084833
chr_2 g5524 g5524.t1 exon g5524.t1.exon9 10084940 10085005
chr_2 g5524 g5524.t1 cds g5524.t1.CDS9 10084940 10085005
chr_2 g5524 g5524.t1 exon g5524.t1.exon10 10086217 10086372
chr_2 g5524 g5524.t1 cds g5524.t1.CDS10 10086217 10086372
chr_2 g5524 g5524.t1 exon g5524.t1.exon11 10086442 10086634
chr_2 g5524 g5524.t1 cds g5524.t1.CDS11 10086442 10086634
chr_2 g5524 g5524.t1 exon g5524.t1.exon12 10086699 10086705
chr_2 g5524 g5524.t1 cds g5524.t1.CDS12 10086699 10086705
chr_2 g5524 g5524.t1 TSS g5524.t1 10086782 10086782
chr_2 g5524 g5524.t1 TTS g5524.t1 NA NA

Sequences

>g5524.t1 Gene=g5524 Length=2100
ATGGGTGATTTATCTTATTCACGGTTATTGTCAGTGTCATCTGATGACGAAAAAGAATTT
GTGACATTAGAAGATTTAAAGGCACATCAATTGACTGATTTGGAGCAGCGATCAAAAGAT
AATTTGAAATTAATTGAACAAAAAGAGGAGCACGATCAAAGTTTTAATGTGTATTATGAT
TTAAATACACACAAGCCAAACAGTGTTAGTAATCTGTATCAAGATATGACAATTGACACA
AGTTTTTTACCTGAATCAGACATCGCACTAATGGACTCATCAAACTCAATAAATACTGAA
AATCTTCAAAATCAGTACATTCAAAAAAGTTCAAGAAAGAGGAAATTTTCATTGTCTGAA
GTAAGTGAAGATATTGAGGACGATGACGCTAAATCGATTAAAACTACAGATGACAATAAA
AAGGCAAATCATTCAGAGATCGAAAAAAGGCGTAGAGATAAAATGAATAATTTCATCACC
GAGCTTTCATCAATGATCCCAATGTGCCATGCCATGTCAAGAAAGTTAGATAAATTGACG
GTCTTACGAATGGCTGTCCAACATTTGAAAACCATTAGAGGCACAACAAATTCCTTCACT
GCAGATTATAAGCCAGCATTTTTATCTGACCAAGAATTAAAAATGTTGATTCTACAAGCT
GCTGAAGGATTTTTATTCGTCGTTGGGTGCGATCGTGGCCGAATTTTATATGTGTCCGAG
TCAGTTTCGGAAGTATTAAATTATACACAAGGAGAACTTTTAGGCCAATCATGGTTTGAC
ATTCTTCATCCGAAAGACATTGCAAAAGTTAAAGAGCAACTAAGTTCATCAGATTTGAGT
CCACGCGAACGTCTCATAGATGCTAAAACAATGTTACCAGTTAAACATTCCGATGTCTCA
ATAGTGACACAAAACATTTTCCCTGGTGCAAGAAGATCATTTTTCTGTCGTATGAAATGT
AAATCGTCTGTTCAAATAAAGGAAGAAATTGATTCAAACAATACAACATCAAATTGCCAT
CGACGAAATAAAAAGCAAATGGCGGACAAGAAATTTGTTACAATTCAGAGCATTGGTTAC
TTAAAGTCATGGGCACCTGCAAAAATTCTAGAAACATCTGAACAAGAATCTGAAGAGGGA
GACTGTCTGTCTTTATCATGCCTTGTAGCTGTGGGAAGATTAGTAGATTACAACAATGAC
GGAAGCTTTCAGAACATAAAAACTACAATTTCAAATAATGCAAAACGAGGAAATCCATCA
TTGAGAAATGTTCATTTCATTTCACGACATGCAAATGATGGGAAATTTTTATTTGTTGAT
CAAAGAGCTACATTAGTGTTAGGATTTCTTCCACAGGAACTTCTTGGTACAAGTATGTAT
GAATATTTTAATCATCGTGATATCGCTGCACTTGCTGACTCTCATAAAGTTGCATTGACG
ACAACAGAAAAAGTTACCACACCAATTTATGGTATGAGAACAAAAGATAATGGTTTTATC
AATATTCAAAGTGAATGGAAGTCATTTAAGAATCCATGGACTAGGGATATTGAATTTTTA
ATTGCAAAAAATAATGTTATCTTTTCTGATTTGCGAAATTATGAAAATGGAAATCAAATT
CGCAATAATGGTAACGAAAGCAGTTATGACTTTTTGAATCAAACAAATGGTCGTGAAATG
ACGAGAATGATTAATGTTCATATCGAGGCAAGTAAAATTGGACGACAAATTGCTGAGCAA
GTGCTTGACTATCAAAGACGTATGGGTGATGATGCTTCACCAGATTCAAGTAGTTCCGAT
CCTGATCCAACACTTGCTATGTCATTAGCAGATGAAGGAAATCATCTTGCTTCCATGAAT
GTAGAAAATAACAGTAATTCTGCTGCATCTAATGATATGCCTACTCGAATCAATGGCACA
TATTCAAACTTTGCAACATTCAATCATGATAGATCAAGTGTTGAAAATGGGACAAATGAA
GTAACAACTGGTGATGGAAATGATGATGCATCAATGGCTGTATTAATGAATTTATTAGAA
GCTGATGCTGGTTTAGGTGGACCAATTGATTTTACAGGACTGCCATGGCCTCTTCCGTAA

>g5524.t1 Gene=g5524 Length=699
MGDLSYSRLLSVSSDDEKEFVTLEDLKAHQLTDLEQRSKDNLKLIEQKEEHDQSFNVYYD
LNTHKPNSVSNLYQDMTIDTSFLPESDIALMDSSNSINTENLQNQYIQKSSRKRKFSLSE
VSEDIEDDDAKSIKTTDDNKKANHSEIEKRRRDKMNNFITELSSMIPMCHAMSRKLDKLT
VLRMAVQHLKTIRGTTNSFTADYKPAFLSDQELKMLILQAAEGFLFVVGCDRGRILYVSE
SVSEVLNYTQGELLGQSWFDILHPKDIAKVKEQLSSSDLSPRERLIDAKTMLPVKHSDVS
IVTQNIFPGARRSFFCRMKCKSSVQIKEEIDSNNTTSNCHRRNKKQMADKKFVTIQSIGY
LKSWAPAKILETSEQESEEGDCLSLSCLVAVGRLVDYNNDGSFQNIKTTISNNAKRGNPS
LRNVHFISRHANDGKFLFVDQRATLVLGFLPQELLGTSMYEYFNHRDIAALADSHKVALT
TTEKVTTPIYGMRTKDNGFINIQSEWKSFKNPWTRDIEFLIAKNNVIFSDLRNYENGNQI
RNNGNESSYDFLNQTNGREMTRMINVHIEASKIGRQIAEQVLDYQRRMGDDASPDSSSSD
PDPTLAMSLADEGNHLASMNVENNSNSAASNDMPTRINGTYSNFATFNHDRSSVENGTNE
VTTGDGNDDASMAVLMNLLEADAGLGGPIDFTGLPWPLP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g5524.t1 CDD cd00130 PAS 223 277 0.0000000
21 g5524.t1 CDD cd00130 PAS 426 521 0.0000000
17 g5524.t1 Gene3D G3DSA:4.10.280.10 HLH 130 195 0.0000000
18 g5524.t1 Gene3D G3DSA:3.30.450.20 - 201 398 0.0000000
19 g5524.t1 Gene3D G3DSA:3.30.450.20 - 416 569 0.0000000
4 g5524.t1 PANTHER PTHR23042 CIRCADIAN PROTEIN CLOCK/ARNT/BMAL/PAS 117 699 0.0000000
5 g5524.t1 PANTHER PTHR23042:SF99 PROTEIN CYCLE 117 699 0.0000000
8 g5524.t1 PRINTS PR00785 Nuclear translocator signature 154 169 0.0000000
12 g5524.t1 PRINTS PR00785 Nuclear translocator signature 174 194 0.0000000
9 g5524.t1 PRINTS PR00785 Nuclear translocator signature 203 226 0.0000000
10 g5524.t1 PRINTS PR00785 Nuclear translocator signature 228 247 0.0000000
7 g5524.t1 PRINTS PR00785 Nuclear translocator signature 260 278 0.0000000
13 g5524.t1 PRINTS PR00785 Nuclear translocator signature 308 321 0.0000000
11 g5524.t1 PRINTS PR00785 Nuclear translocator signature 352 371 0.0000000
6 g5524.t1 PRINTS PR00785 Nuclear translocator signature 386 402 0.0000000
1 g5524.t1 Pfam PF00010 Helix-loop-helix DNA-binding domain 140 191 0.0000000
3 g5524.t1 Pfam PF08447 PAS fold 235 274 0.0000011
2 g5524.t1 Pfam PF14598 PAS domain 426 527 0.0000000
26 g5524.t1 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 139 192 16.6090000
28 g5524.t1 ProSiteProfiles PS50112 PAS repeat profile. 210 274 15.0610000
27 g5524.t1 ProSiteProfiles PS50112 PAS repeat profile. 433 482 10.7470000
22 g5524.t1 SMART SM00353 finulus 145 198 0.0000000
23 g5524.t1 SMART SM00091 pas_2 212 279 0.0000000
24 g5524.t1 SMART SM00091 pas_2 414 480 0.0002700
16 g5524.t1 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 138 221 0.0000000
15 g5524.t1 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 222 323 0.0000000
14 g5524.t1 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 426 525 0.0000000
25 g5524.t1 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 231 276 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.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5524.t1.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