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 g5012 g5012.t3 TSS g5012.t3 6444628 6444628
chr_2 g5012 g5012.t3 isoform g5012.t3 6445003 6449697
chr_2 g5012 g5012.t3 exon g5012.t3.exon1 6445003 6445052
chr_2 g5012 g5012.t3 cds g5012.t3.CDS1 6445003 6445052
chr_2 g5012 g5012.t3 exon g5012.t3.exon2 6449432 6449697
chr_2 g5012 g5012.t3 cds g5012.t3.CDS2 6449432 6449696
chr_2 g5012 g5012.t3 TTS g5012.t3 6449671 6449671

Sequences

>g5012.t3 Gene=g5012 Length=316
ATGGGCTCAAGACAAGTGGTAGCCAATAAAATGGCAAATCCACAATCATGGTGGTACTTA
GCATTATTAATCTCATTTATGATTGTAAATACAAGTGCTCAAATGTGGAATGAAGTAGAG
AGCAGTGGTATAGGATTAACAGGAAGATCGAGGAATAGGCAGCCATTTAGAGAAAATGTA
CAAAGAGTGCCAGACTCTTATGATATTGTAGACACTGCCAGTGCACAAGTCAGAGGCCCA
CCTGCTAAAAATTGTACAGGCTCTGGTTGTTGTATACCAAAATGTTTTGCAGAAAAAGGA
AATAGAGGATTACCAG

>g5012.t3 Gene=g5012 Length=105
MGSRQVVANKMANPQSWWYLALLISFMIVNTSAQMWNEVESSGIGLTGRSRNRQPFRENV
QRVPDSYDIVDTASAQVRGPPAKNCTGSGCCIPKCFAEKGNRGLP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g5012.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 15 -
5 g5012.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 16 33 -
3 g5012.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 34 105 -
2 g5012.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 33 -
1 g5012.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 17 36 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5012/g5012.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5012.t3.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