Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein similar.

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_3 g1184 g1184.t18 TTS g1184.t18 8579756 8579756
chr_3 g1184 g1184.t18 isoform g1184.t18 8579757 8590729
chr_3 g1184 g1184.t18 exon g1184.t18.exon1 8579757 8580304
chr_3 g1184 g1184.t18 cds g1184.t18.CDS1 8580159 8580304
chr_3 g1184 g1184.t18 exon g1184.t18.exon2 8582927 8583033
chr_3 g1184 g1184.t18 cds g1184.t18.CDS2 8582927 8583033
chr_3 g1184 g1184.t18 exon g1184.t18.exon3 8583097 8583266
chr_3 g1184 g1184.t18 cds g1184.t18.CDS3 8583097 8583266
chr_3 g1184 g1184.t18 exon g1184.t18.exon4 8583332 8583553
chr_3 g1184 g1184.t18 cds g1184.t18.CDS4 8583332 8583553
chr_3 g1184 g1184.t18 exon g1184.t18.exon5 8583625 8583845
chr_3 g1184 g1184.t18 cds g1184.t18.CDS5 8583625 8583845
chr_3 g1184 g1184.t18 exon g1184.t18.exon6 8583922 8584107
chr_3 g1184 g1184.t18 cds g1184.t18.CDS6 8583922 8584000
chr_3 g1184 g1184.t18 exon g1184.t18.exon7 8590275 8590729
chr_3 g1184 g1184.t18 TSS g1184.t18 8590731 8590731

Sequences

>g1184.t18 Gene=g1184 Length=1909
GTGTTACCTTTACTTATTTAAAACGCCATTGTAAAAAAATTGTGCTGATAAAAATATTCA
AAATAAATAATTACACTCACTAAATGAGTGTCGTAAACTAGTGAAAAACGTTATTGACAT
AGTGAAAAACTAAAAAATCATTAGAGCATATGTTTGGCAGTGACCAAAAGTGCTTAAAAC
TGATTTGAAAGTGTTCAGCTAATCATATTATTGTTCGGACTATAAAAAAGGAATTTTTAA
ATATTTTGATTGTGTCAATCTGTCGTCTCAAATTCTTGATTAGTAACAGATAAAGACCGA
GTGATTGTTTCTTAAACTAATTTGAATGAGAACATCAGTTTATGAGTGCTGAAAATGTGT
AAAATAAATCGAAATTCAGAACTTGAATCAACAACGAATAGTCTGAAGGCTATCTCTGTA
ACCATCCAAAAGCCAAAGGAAAAAGAGAAGAGAAGGAACAATGAAAAACGCAAAGAAAAG
TCTCGCGATGCAGCAAGATGCCGTCGTTCGAGAGAAACAGAGATATTTACGGAACTTGCA
AATTCACTTCCAATAAAACAAGATGAAATTGATCATCTTGACAAAGCTTCTGTTATGCGT
CTTTCCATTTCTTATCTCAAGATTCGTAATATGCTTGAGTTTTCCAAAAATTAAAAATTT
GGATATTCCCGTTGCTGAGCTCGAAAATGGTGATGAAACAGATGAGGATGTTAAGGATGT
CAAGATTGACGTTTTGAGAAAAATTGTTGAGGATGAGAAATTTGCTCTAAAAGCACTCGA
TGGATTCTTGCTTGTGCTCAATGCTGAAGGCGATATTACATATGTATCGCAAAACATTGC
AGAATACCTGGGTCTAGCAAAAATTGATTTATTGGGTCAACCGATATGGGACTACACACA
TGCGTGTGATCACGATGAACTTCGTGAAGCTCTTAATGGCCGCAAAACTTCACCGTCTGA
AGTTGTTAATGGCGCAAAATCAGCTGATTGTAATCCATTATTACATCGTGATATGATGAT
TCGTTTGAAATGCACACTTACAAAGAGTGGACGTTTTGTTAACATCAAAAGTGCTTCTTA
TAAGGTGATTCATTTGACGGGTCATATTGTGTTCAAAGATGATGGCTATCGTCAATTGTT
GGCAATTGGTCGGCCACTAGCTCATCCATCAAATATCGAGGTGCCTTTGGGTTCCAGCAC
TTTTCTTACAAAACATACATTAGATATGAAATTCAGCTTTGTCGATAGTCCAAAAATGTT
TGAGCTGATGGGGTACAAACCTGAACATTTGTTGGGCAAATCGCTTTATGAATATCATCA
TGGTAGCGATTCGGAGAGTCTCATGTCAAGTTTCAAGTGCCTAATCAGCAAAGGTCAAAC
TGAAACTAACCGCTACCGATTTTTGGCACGTAATGGTGGTTACGTTTGGATCGTAACTCA
AGCAACTGTAGTGTTCGAGAAACAGAAGCCCCAAAGTGTCGTCTGCGTTAGTTACGTTGT
GAGGTGAGTACAATGAAATTTTTTATTCTTTTATGATTATCGTCGTGGTCAATTTAATTG
ATATATGTGTGCATTGTGACCATTTCTCTTTTTATATATGCGTTTATTTATCTACTGATC
GTCCTACTTAAAATGTCAATCAGTCAGTCAATTTCAATCGCGTTTATACATAAAGACATT
AAGGGGACGATCCATGATTATTATACAACAATCGATAAAATAAAGTTGGCTGTGATGATG
TGGTGGTTATAAAAAATTACTATAGTAAAAAGAAGAAGAAGTGGAATACAAGTAGAAATT
AAGTGCTACCACTTGTGAAAATGAGAGTCTATAGTTGTCTGAAAGCCAAATTCCTTTGTT
CCCTTTAATAACAATAATAAACTTTTATTGATTCACTTGGTTTTTAAAG

>g1184.t18 Gene=g1184 Length=314
MKLIILTKLLLCVFPFLISRFVICLSFPKIKNLDIPVAELENGDETDEDVKDVKIDVLRK
IVEDEKFALKALDGFLLVLNAEGDITYVSQNIAEYLGLAKIDLLGQPIWDYTHACDHDEL
REALNGRKTSPSEVVNGAKSADCNPLLHRDMMIRLKCTLTKSGRFVNIKSASYKVIHLTG
HIVFKDDGYRQLLAIGRPLAHPSNIEVPLGSSTFLTKHTLDMKFSFVDSPKMFELMGYKP
EHLLGKSLYEYHHGSDSESLMSSFKCLISKGQTETNRYRFLARNGGYVWIVTQATVVFEK
QKPQSVVCVSYVVR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g1184.t18 CDD cd00130 PAS 72 124 1.58445E-11
14 g1184.t18 CDD cd00130 PAS 211 309 2.68304E-14
7 g1184.t18 Gene3D G3DSA:3.30.450.20 - 60 200 1.5E-29
8 g1184.t18 Gene3D G3DSA:3.30.450.20 - 201 314 3.1E-27
3 g1184.t18 PANTHER PTHR23043 HYPOXIA-INDUCIBLE FACTOR 1 ALPHA 58 313 1.7E-123
4 g1184.t18 PANTHER PTHR23043:SF17 PROTEIN SIMILAR 58 313 1.7E-123
1 g1184.t18 Pfam PF00989 PAS fold 68 125 1.5E-7
2 g1184.t18 Pfam PF08447 PAS fold 229 309 3.8E-15
10 g1184.t18 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
11 g1184.t18 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g1184.t18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
13 g1184.t18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 20 -
9 g1184.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 314 -
21 g1184.t18 ProSiteProfiles PS50112 PAS repeat profile. 68 125 14.159
20 g1184.t18 ProSiteProfiles PS50112 PAS repeat profile. 229 271 11.359
17 g1184.t18 SMART SM00091 pas_2 63 129 4.2E-11
16 g1184.t18 SMART SM00091 pas_2 202 269 0.016
6 g1184.t18 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 72 126 9.95E-13
5 g1184.t18 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 214 313 5.89E-20
18 g1184.t18 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 76 131 7.9E-6
19 g1184.t18 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 229 308 2.5E-7

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:0005515 protein binding MF
GO:0006355 regulation of transcription, DNA-templated BP

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