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 g5704 g5704.t2 isoform g5704.t2 11299772 11323095
chr_2 g5704 g5704.t2 exon g5704.t2.exon1 11299772 11300507
chr_2 g5704 g5704.t2 cds g5704.t2.CDS1 11299962 11300210
chr_2 g5704 g5704.t2 exon g5704.t2.exon2 11309282 11309511
chr_2 g5704 g5704.t2 exon g5704.t2.exon3 11313508 11313647
chr_2 g5704 g5704.t2 exon g5704.t2.exon4 11322912 11323095
chr_2 g5704 g5704.t2 TSS g5704.t2 NA NA
chr_2 g5704 g5704.t2 TTS g5704.t2 NA NA

Sequences

>g5704.t2 Gene=g5704 Length=1290
TCAGAATTGCGATATTTTTGATTCGCTTGGCGTGAGGGTTGTCGGTGAATTGGTAAGCGA
TGAAGGTGATAAAGATGATGAGGATAAGCTCGATGTTGACATAGTTGAAGGTGATGAACA
TTCATCGTTGTTGTTATTATTGATACAATTACTCGTTGATGATCCATTATCATTTTCACA
GGCCTCATTTATGACTATCATATTCTTTGATGCTGCTGATGTCATCTCAACATCTTCATC
AGAACTCGTTGGTTCAGGTGATCTCATCAGACAATTATTATTACGGCTATTACTATTGTT
GTTATTATTATTGTTATTGTTGTCGTCGTTGGGCACTCGTAGTGTCAATTTGTTCTTATT
AAATAGATTTTTGCGATTGCGACACGGAAGCGTTAGTGGAAATGGCGGTGGTTGTGTCGA
TGACGATGTTGTTCTTTGATGATGCGGCTCTTCTATAAGAAATGGATGTTGACTCGTTTG
TGGTACTGCTTGATTAGCAAGTGGCTGTGGTCTTAGCATTCCATCTGCAATGAGGCTCTG
CTCTAGCTCTAGCAATTGACCCATAAAGTTTAAATTCGGCGAAATAATTGGGCGTGCGAC
TTTCACAAGTTGATACGCCTCAAGAAGGGAAAGCGATTTGTATCGCATCACATAGGCAAT
GGCAATTGTCGCTGAACGTGATATTCCAGCTTGACAATGCAACAACACTGTTGATCCTTT
TTTACGGGCTTCCTCTGATAAATTCAAATGCCTCTTGAAAGTATTGCTTAATGTTCTGAT
GTGGTGTATCATTTGCAGGAATCTGTTTGTACTTGACGCCAGGCGTTATTTGTGTTGTAT
TTGATGGTGACTGACATGTTACATTAAGGACACAATTGGCACCGACACTCGATGGATCGA
TGGCATCTCGTCCATTACCTAGTAGAAGATGTGGAAAAACTGGTGACGCTGGATGTGTTT
CAATATCATGTGAAACTGCTGGACTAGAGCAACTGCGTGATAGAGGAATCCTTGAGCTAT
TTGGTGTCAGAGACGAATCATCACAGTGTCTTTTATTCATGCTCGTTGATGTGCCGCAAT
TTGAATTTGATGCATTGTTGTTATCTATTTATTTTATTTCTTAGATTTCCTTATATTTGT
TATCAAAATGGAGGTGGAGCTTTTCTTATTCCTTACGTCATTATGTTGCTTCTTGGTGGA
TTGGTAAGAAAATTTTTGTTTTCACTATCTCTTTATGGTTTTCACTAAATTTAAAATTTC
AATAATTGCTTTGTTTACTTTTTTAAAAGC

>g5704.t2 Gene=g5704 Length=82
MTIIFFDAADVISTSSSELVGSGDLIRQLLLRLLLLLLLLLLLLSSLGTRSVNLFLLNRF
LRLRHGSVSGNGGGCVDDDVVL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g5704.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 28 -
4 g5704.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 29 57 -
2 g5704.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 58 82 -
1 g5704.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 35 57 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5704/g5704.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5704.t2.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.

Raw TPM values