Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g504 g504.t2 isoform g504.t2 3816624 3817835
chr_3 g504 g504.t2 exon g504.t2.exon1 3816624 3816626
chr_3 g504 g504.t2 cds g504.t2.CDS1 3816624 3816626
chr_3 g504 g504.t2 exon g504.t2.exon2 3816695 3816786
chr_3 g504 g504.t2 cds g504.t2.CDS2 3816695 3816786
chr_3 g504 g504.t2 exon g504.t2.exon3 3816842 3817065
chr_3 g504 g504.t2 cds g504.t2.CDS3 3816842 3817065
chr_3 g504 g504.t2 exon g504.t2.exon4 3817118 3817164
chr_3 g504 g504.t2 cds g504.t2.CDS4 3817118 3817164
chr_3 g504 g504.t2 exon g504.t2.exon5 3817230 3817835
chr_3 g504 g504.t2 cds g504.t2.CDS5 3817230 3817679
chr_3 g504 g504.t2 TTS g504.t2 3817937 3817937
chr_3 g504 g504.t2 TSS g504.t2 NA NA

Sequences

>g504.t2 Gene=g504 Length=972
ATGACTTCGGTTTTCCTTATTAAATTGGATGGTAGTCAAGAAAAACTCAAATATAGTTTT
CAAAAAATTTATAAACAGAAAGATTTTGGAACATGGACAATTTCGATCACTGCTACTCCG
AAGGAATTTTCAGGGATGGTTAATTTGACGCCAAATAATTTTAATACATACATTTATGCT
GATCAAATACAAATTAAGACTATAATACGCGAGCTTAAAAATAATAATCCTGAGAGATTA
GAAGAAAAGTATCGTGCTATTGAGATTAAAGCAAAATTACATTCTGAGCTAATTTATATC
TTTGACTTTAAATATTTTGTTAAAAATTCGCCATCATTGTACATACCGAAATCACTTATT
CTAATGATTGAGATACCAGCTATTCCATTTGTATTAAATACCAAAGAAATCCAAAAATTG
AAAAGTATTTGTGACAAAAAAATTAACTGTGATGTTACATTAATGGTTCGAGATAAAGAG
CTCAAAGCACATAAAGCCGTTTTGGAAAAATGTAAAGTTTTCAAAAAAATGTTTGAAGAA
AATCCTGATGTTATTCAAATTAATGACGTTGATTATGATGTTTTAATAGAAATGTGTCGC
TTTTTATACTGTAATGAAATTTTCTACAAAAATATACTAACTCTAAAACTCATCGTGGCA
GCTAAAAACTACATGATAACTGATCTTGTTCAAAAGTGCGAAGAATATCTGATTGATCAC
ATAGATTTTTACAACGTCATCAATATTTTAATACAAGCTGATGCATTGAAAATGGACAGG
ATGCGTAATGCTGCAATTGAGTTTATCATCATGTAAGAATTCTTCCTTTCTTTTTTCATT
GTTTCTTTCATTATTATCTCTTTTAGCAATCGTGAAATAATTTATCTCACTCAAGATTGG
TCAGAGTTCGAAAAGAATCATAAAGCTTTAGTTCTGTTAATCGGAGAAAAAATTATATGC
AAAGTTACTTGA

>g504.t2 Gene=g504 Length=271
MTSVFLIKLDGSQEKLKYSFQKIYKQKDFGTWTISITATPKEFSGMVNLTPNNFNTYIYA
DQIQIKTIIRELKNNNPERLEEKYRAIEIKAKLHSELIYIFDFKYFVKNSPSLYIPKSLI
LMIEIPAIPFVLNTKEIQKLKSICDKKINCDVTLMVRDKELKAHKAVLEKCKVFKKMFEE
NPDVIQINDVDYDVLIEMCRFLYCNEIFYKNILTLKLIVAAKNYMITDLVQKCEEYLIDH
IDFYNVINILIQADALKMDRMRNAAIEFIIM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g504.t2 Gene3D G3DSA:3.30.710.10 Potassium Channel Kv1.1; Chain A 132 270 0.000
2 g504.t2 PANTHER PTHR24413:SF213 FI01029P-RELATED 126 269 0.000
3 g504.t2 PANTHER PTHR24413 SPECKLE-TYPE POZ PROTEIN 126 269 0.000
1 g504.t2 Pfam PF00651 BTB/POZ domain 142 239 0.000
7 g504.t2 ProSiteProfiles PS50097 BTB domain profile. 150 211 15.163
5 g504.t2 SMART SM00225 BTB_4 150 241 0.000
4 g504.t2 SUPERFAMILY SSF54695 POZ domain 137 241 0.000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g504/g504.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g504.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding 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. There were no conditions that were differentially expressed