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_2 g5885 g5885.t4 isoform g5885.t4 12585866 12587488
chr_2 g5885 g5885.t4 exon g5885.t4.exon1 12585866 12586899
chr_2 g5885 g5885.t4 cds g5885.t4.CDS1 12586568 12586867
chr_2 g5885 g5885.t4 exon g5885.t4.exon2 12587023 12587067
chr_2 g5885 g5885.t4 exon g5885.t4.exon3 12587120 12587228
chr_2 g5885 g5885.t4 exon g5885.t4.exon4 12587363 12587488
chr_2 g5885 g5885.t4 TSS g5885.t4 NA NA
chr_2 g5885 g5885.t4 TTS g5885.t4 NA NA

Sequences

>g5885.t4 Gene=g5885 Length=1314
ATCCGTATCAACTTTTAAATGCCACGTCGCGTTTGGTTAATTCGGGATCTGGGCAGATAC
AATTATGGCAATTTTTGTTAGAGCTTCTCGCTGATTCGTCGAATTCTGATTTTATAAAGT
GGGAGGGAACTGCTGGTGAATTTAAATTAATCGATCCAGATGAGGTGGCGAGACGATGGG
GTGTTAAGAAAAATAAAACAAATATGAATTATGATAAACTAAGTCGTGCATTGAGATATT
ATTATGATAAATCAATCATGACGAAAGTACATGGAAAAAGTAAATTTAAATAGGTTTGAC
TTTCATGGATTAATGGCAGCTTGTCATGCACAAGCACAAGGATGTGATTCAACAAGTATG
CTTCCAAAATACCCTCCACATCTCCTTATGCCAAATGATTTTTCAAGTTATGCAAGCACA
TCGACTGCCATTCCTACAAGTACAAATCAAGTATCAGCAGCATTGTCATCATCTTTCAAA
CCAGTACAACCAATCATTACTCCTCATGCAACTCCTTCTACTTCTTCATCATCGTCATCA
CCATCGACAGTGGCACAAACACCAAACACTGAAAGAATACCTGGATGGCCATATTTACCC
TCAAACTTTTAAACAATTGAAATCTCAAATAATTTGTAAATGACATCGTTTTAATTGTCA
GCATATAAAAGGCTATTCTGATCTCAAATTGTGAATTTATTATTATTTTTCCTTTAATTT
CAGTCCCTTTTCCTTTTCTATTGTTTCAATTTTCTGTTCTTTCCTCCAGTGAATTACATT
TTTTTATACAAACATCACATGAATAATTTTTATACGTAAGTCTGTGTAGCAATAATTAAA
ACTTTTTTTAATTTTAAAAATACATTCTTAATGAAGATATTGATACCTCAGCTGTTAGAT
AATAAGAAGAACAATTTAAATTTAAATCAAATGCTCAAAACTATAAAAAAAGTTCATGTG
ACAAATCTCTTTATGTCTCTTCTTTTAGTGTTGAGAATATGAAAGAATGTTGTAATTAGA
TAATAAGTAGATGTTTTTTGTAATTATTCAAATCCTAATCAAATTATCTTAATATAATGA
TTAGAAATAAATCAGTGAATTAATAAAAGAACATGTTTAAAAGAAATATGCATTTTTATG
CGAAACGTTTTCAGAATCGGTAAAATGAGAAACGCTACTCAAATAAAACATGTTGTGCAA
CATTTTCTTCCCTCTTTTTTGTTACGTCTCATAGAGTCTCATAAACATACTTTGTGCATG
ACACATTTAACTGAAATTTTACAACGGTAAAGAAGAAAACTATTGAATATTATT

>g5885.t4 Gene=g5885 Length=99
MAACHAQAQGCDSTSMLPKYPPHLLMPNDFSSYASTSTAIPTSTNQVSAALSSSFKPVQP
IITPHATPSTSSSSSSPSTVAQTPNTERIPGWPYLPSNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
g5885.t4 MobiDBLite mobidb-lite consensus disorder prediction 60 99 -
g5885.t4 MobiDBLite mobidb-lite consensus disorder prediction 60 86 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5885/g5885.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5885.t4.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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