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 g5325 g5325.t15 TSS g5325.t15 8861795 8861795
chr_2 g5325 g5325.t15 isoform g5325.t15 8861899 8862938
chr_2 g5325 g5325.t15 exon g5325.t15.exon1 8861899 8861926
chr_2 g5325 g5325.t15 cds g5325.t15.CDS1 8861899 8861926
chr_2 g5325 g5325.t15 exon g5325.t15.exon2 8862012 8862070
chr_2 g5325 g5325.t15 cds g5325.t15.CDS2 8862012 8862070
chr_2 g5325 g5325.t15 exon g5325.t15.exon3 8862137 8862216
chr_2 g5325 g5325.t15 cds g5325.t15.CDS3 8862137 8862216
chr_2 g5325 g5325.t15 exon g5325.t15.exon4 8862284 8862938
chr_2 g5325 g5325.t15 cds g5325.t15.CDS4 8862284 8862425
chr_2 g5325 g5325.t15 TTS g5325.t15 8862940 8862940

Sequences

>g5325.t15 Gene=g5325 Length=822
ATGCAACAACCTACAGTAATAATTCAACATTCAAATGTTGCTGTTGGACCAAATTCAACT
CGACTCACTTGCCCATCATGTCATGCAGTAATTTCTACGCGTGTTGAACGTAAATCATCG
GCTAAAACTTATATAGTTGCGGTACTTCTATGTGTGTTCTTATGCTGGCCATGTGTATGC
GTTCCGTTTTGCACAAATTCCTGCCGGAATGCTAACCATTATTGCCCCAATTGGTATGTA
TCTAAAACAAGATTAGGCTTAAGTCAAGTAAGATTAGTGTTAAGTCAAGTGATAAGTCAA
GTCAAGTAATAAATTCAAGTTAAAAATATTCAATTCAAGTTAAAACTGAAATCTAACAAA
ATTAGAAATTTTCATAATCAAAATGCGCTATTGTCACATTAATAATTGCTAATAATATTC
TCTTTTATTTACAGCAAAGCATTCTTGGGAACCTACAACTGAAAATTCAAGGTATTATTC
ATCTGTATTACTTCATTAATTTTTAAGTTAAAAAGAGTTCGATTTGCTCCATTAGATATT
AAGATTGTGCTCCAAAAAGTGAATCATATAAAGCAAATTACTAATTCATTCTAGAAACAA
GTGCTATATAAGAAAATTTATTTATCATAAACAAGATAACAACGACTGTCTCATTACGAA
ATGAGTGCGAATATTGTCAGGTGATAAGAATATTTATTTTTTACTTACTTAATTGTCGCA
TTCAAAGATAAAAACGTAATAAAAGTTAAAAGAAGTTAGAACAAAAATTTTGATTTTAAA
TGTTAAAAATAATGAATTTAATAAAAAATATTTTTTAAAAAT

>g5325.t15 Gene=g5325 Length=102
MQQPTVIIQHSNVAVGPNSTRLTCPSCHAVISTRVERKSSAKTYIVAVLLCVFLCWPCVC
VPFCTNSCRNANHYCPNWYVSKTRLGLSQVRLVLSQVISQVK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5325.t15 PANTHER PTHR23292:SF14 FI16615P1-RELATED 2 77 9.8E-27
3 g5325.t15 PANTHER PTHR23292 LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR 2 77 9.8E-27
1 g5325.t15 Pfam PF10601 LITAF-like zinc ribbon domain 18 77 1.1E-18
8 g5325.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 43 -
9 g5325.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 44 64 -
7 g5325.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 65 102 -
6 g5325.t15 ProSiteProfiles PS51837 LITAF domain profile. 3 90 16.83
5 g5325.t15 SMART SM00714 litaf 19 84 3.4E-9
4 g5325.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 43 65 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5325/g5325.t15; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5325.t15.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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