Gene loci information

Transcript annotation

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

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_1 g14012 g14012.t2 TSS g14012.t2 33981622 33981622
chr_1 g14012 g14012.t2 isoform g14012.t2 33981724 33983445
chr_1 g14012 g14012.t2 exon g14012.t2.exon1 33981724 33981761
chr_1 g14012 g14012.t2 cds g14012.t2.CDS1 33981724 33981761
chr_1 g14012 g14012.t2 exon g14012.t2.exon2 33982122 33982798
chr_1 g14012 g14012.t2 cds g14012.t2.CDS2 33982122 33982798
chr_1 g14012 g14012.t2 exon g14012.t2.exon3 33982932 33983219
chr_1 g14012 g14012.t2 cds g14012.t2.CDS3 33982932 33983219
chr_1 g14012 g14012.t2 exon g14012.t2.exon4 33983295 33983445
chr_1 g14012 g14012.t2 cds g14012.t2.CDS4 33983295 33983443
chr_1 g14012 g14012.t2 TTS g14012.t2 NA NA

Sequences

>g14012.t2 Gene=g14012 Length=1154
ATGGAGGAATCTACGGTCGATAAAGAGCGATATGCGAGTCGAGAGAACCATTGTGAAATT
GAGAGAAGACGACGTAATAAAATGACAGCTTACATTACTGAACTCTCTGATATGGTGCCG
ACATGCAGCGCTCTTGCTCGAAAACCTGATAAACTTACAATTTTAAGAATGGCAGTTGCA
CATATGAAAGCACTTCGAGGCACAGGCAATACAAATACAGATGGAAGCTACAAACCATCT
TTTCTAACAGATCAAGAGTTGAAGCATTTAATTTTGGAAGCAGCTGATGGATTTCTATTT
GTTGTGTCATGCGACACTGGTCGTATTATATACGTCTCAGATTCAGTTGCACCTGTTTTG
AATCACTCACAAAATGACTGGTATGGTTCATCTCTTTTTGAATTAGTGCATCCAGACGAT
ATTGAAAAAGTTCGTGAGCAATTATCCACACAAGAACCACAAAATTCTGGTCGTATTTTG
GACTTAAAAACTGGAACTGTCAAAAAAGAAGGCCATCAATCATCAATGAGATTGTGCATG
GGATCACGCAGAGGCTTCATTTGTCGAATGAAAATTGGAAATATCAATCCAGAGAACATG
GCCGTTGGGCATCTTAATCGATTGAAACAACGCAATTCTCTCGGACCTTCTAGAGATGGA
CAAAACTATGCAGTTGTTCATTGCACTGGATATATTAAAAACTGGCCACCGACTGGCGTA
CAACTCGATCGGCAAAATGAAGATGACTTACATTCCTCACATTGCTGCTTGGTCGCTATC
GGTCGTTTACAAGTTACATCGACTGCAAATTCTGCTGATTTAAATGGTTCCAATAATCAA
TCTGAATTTATTTCTCGTCACTCAATGGATGGCAAATTTTCATTTGTTGATCAACGTGTC
ATGAACATACTTGGATATGTTCCCACTGATTTATTAGGAAAAAGCTGCTACGATTTTTTC
CATCCTGAAGATCAGAATCATATGAAAGAAAATTTTGATCAAGTTCTCAAGCAAAAAGGA
CAAATGTTTTCCGTCATGTATCGTTTTCGTGCTAAAAATCGAGAATGGGTCTGGCTTCGC
ACCCAAGCATATGCATTTTTAAATCCTTACAATGACGAAGTGGAATATATTGTTTGCACA
AATAGTTCTGCAAA

>g14012.t2 Gene=g14012 Length=384
MEESTVDKERYASRENHCEIERRRRNKMTAYITELSDMVPTCSALARKPDKLTILRMAVA
HMKALRGTGNTNTDGSYKPSFLTDQELKHLILEAADGFLFVVSCDTGRIIYVSDSVAPVL
NHSQNDWYGSSLFELVHPDDIEKVREQLSTQEPQNSGRILDLKTGTVKKEGHQSSMRLCM
GSRRGFICRMKIGNINPENMAVGHLNRLKQRNSLGPSRDGQNYAVVHCTGYIKNWPPTGV
QLDRQNEDDLHSSHCCLVAIGRLQVTSTANSADLNGSNNQSEFISRHSMDGKFSFVDQRV
MNILGYVPTDLLGKSCYDFFHPEDQNHMKENFDQVLKQKGQMFSVMYRFRAKNREWVWLR
TQAYAFLNPYNDEVEYIVCTNSSA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g14012.t2 CDD cd18947 bHLH-PAS_ARNT 8 73 0.0000
23 g14012.t2 CDD cd00130 PAS 95 188 0.0000
22 g14012.t2 CDD cd00130 PAS 281 378 0.0000
18 g14012.t2 Gene3D G3DSA:4.10.280.10 HLH 2 68 0.0000
19 g14012.t2 Gene3D G3DSA:3.30.450.20 - 75 270 0.0000
20 g14012.t2 Gene3D G3DSA:3.30.450.20 - 274 384 0.0000
4 g14012.t2 PANTHER PTHR23042:SF6 ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR 2 3 382 0.0000
5 g14012.t2 PANTHER PTHR23042 CIRCADIAN PROTEIN CLOCK/ARNT/BMAL/PAS 3 382 0.0000
7 g14012.t2 PRINTS PR00785 Nuclear translocator signature 27 42 0.0000
10 g14012.t2 PRINTS PR00785 Nuclear translocator signature 47 67 0.0000
14 g14012.t2 PRINTS PR00785 Nuclear translocator signature 77 100 0.0000
6 g14012.t2 PRINTS PR00785 Nuclear translocator signature 102 121 0.0000
12 g14012.t2 PRINTS PR00785 Nuclear translocator signature 134 152 0.0000
9 g14012.t2 PRINTS PR00785 Nuclear translocator signature 180 193 0.0000
11 g14012.t2 PRINTS PR00785 Nuclear translocator signature 223 242 0.0000
13 g14012.t2 PRINTS PR00785 Nuclear translocator signature 255 271 0.0000
8 g14012.t2 PRINTS PR00785 Nuclear translocator signature 282 299 0.0000
2 g14012.t2 Pfam PF00010 Helix-loop-helix DNA-binding domain 14 65 0.0000
1 g14012.t2 Pfam PF00989 PAS fold 89 191 0.0000
3 g14012.t2 Pfam PF14598 PAS domain 281 382 0.0000
29 g14012.t2 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 12 65 16.5140
31 g14012.t2 ProSiteProfiles PS50112 PAS repeat profile. 84 155 14.3530
30 g14012.t2 ProSiteProfiles PS50112 PAS repeat profile. 288 339 16.9920
24 g14012.t2 SMART SM00353 finulus 18 71 0.0000
26 g14012.t2 SMART SM00091 pas_2 86 153 0.0000
25 g14012.t2 SMART SM00091 pas_2 271 337 0.0000
27 g14012.t2 SMART SM00086 pac_2 344 382 0.0025
17 g14012.t2 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 14 97 0.0000
16 g14012.t2 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 96 239 0.0000
15 g14012.t2 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 282 381 0.0000
28 g14012.t2 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 287 363 0.0000

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. There were no conditions that were differentially expressed