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 g5813 g5813.t2 isoform g5813.t2 12041506 12042289
chr_2 g5813 g5813.t2 exon g5813.t2.exon1 12041506 12041880
chr_2 g5813 g5813.t2 cds g5813.t2.CDS1 12041507 12041880
chr_2 g5813 g5813.t2 exon g5813.t2.exon2 12041941 12042289
chr_2 g5813 g5813.t2 cds g5813.t2.CDS2 12041941 12042289
chr_2 g5813 g5813.t2 TSS g5813.t2 12042304 12042304
chr_2 g5813 g5813.t2 TTS g5813.t2 NA NA

Sequences

>g5813.t2 Gene=g5813 Length=724
ATGACAAACAACGAAATTCAATGGGATTGGAAAGAATTTTGTGAGACTGGTCTCAATGTT
TCAACAAATTCAAGTTCGATAACTCCCTGTGGACAGCAAATTTATATTCATCTGCCAACT
TTCTCACTTTTGGCAATAATTAGTTCATATAATTATGGAAAACTCATTGATCCAGTTTTG
AGGAATAATACTCAAAAATGGTGTCTTAGCATAAGAGCGCTATTAGTCATAGTGTTAGCA
ATTTTACCTCTTATCAAACTACTCACTGAGATGCAAAATGGTGAAAAAATTTGGCCGGTT
GATGTTTTATTAGCATGCACTGAAGCTTTATGCTGGACTATTCATTTTGCATTTCTCGCG
TTATATAGAAAGTTGGGAAAACTGAGTCATCGCGGTCCACTATTGATTTTAATTCTCTAT
TCTTGCTCGCTTTCATTATCAGTACTCTGGGTTCAAACAAATATGAACATTTTTAGTGAA
CTTCGAGTTGCTTTGAATGTTTTTTATGCATTGACATTGCTGCCCAGAGGAAAGTCACAA
TATATGCGTAGAACAATAGAAATAAATGAGCATGAACCATTAATCAACACGTACCATCGT
TTATCAGTTGATGGAAATGAAGAAGATTATATATTAGGCCCTGCTGAAGATGGATATAAT
TTTCTTAGTCGTTTAATCTTTTATTGGGTTAATCCATTAATACAGAAAGCATCGGCTGTA
AAAC

>g5813.t2 Gene=g5813 Length=241
MTNNEIQWDWKEFCETGLNVSTNSSSITPCGQQIYIHLPTFSLLAIISSYNYGKLIDPVL
RNNTQKWCLSIRALLVIVLAILPLIKLLTEMQNGEKIWPVDVLLACTEALCWTIHFAFLA
LYRKLGKLSHRGPLLILILYSCSLSLSVLWVQTNMNIFSELRVALNVFYALTLLPRGKSQ
YMRRTIEINEHEPLINTYHRLSVDGNEEDYILGPAEDGYNFLSRLIFYWVNPLIQKASAV
K

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 33 -
15 g5813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 34 55 -
5 g5813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 56 66 -
14 g5813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 67 85 -
10 g5813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 86 96 -
11 g5813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 122 -
7 g5813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 123 133 -
13 g5813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 151 -
8 g5813.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 152 156 -
12 g5813.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 157 174 -
6 g5813.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 175 241 -
4 g5813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 34 56 -
3 g5813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 68 85 -
2 g5813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 100 122 -
1 g5813.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 134 153 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5813/g5813.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5813.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. There were no conditions that were differentially expressed