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 g5606 g5606.t2 isoform g5606.t2 10587245 10588371
chr_2 g5606 g5606.t2 exon g5606.t2.exon1 10587245 10587853
chr_2 g5606 g5606.t2 cds g5606.t2.CDS1 10587633 10587853
chr_2 g5606 g5606.t2 exon g5606.t2.exon2 10587920 10588371
chr_2 g5606 g5606.t2 cds g5606.t2.CDS2 10587920 10588211
chr_2 g5606 g5606.t2 TSS g5606.t2 10588400 10588400
chr_2 g5606 g5606.t2 TTS g5606.t2 NA NA

Sequences

>g5606.t2 Gene=g5606 Length=1061
ATGTCTGGAGGTAAGAAGTATTGTTGAAAGAAAAATTTACAGTTGCATCAATAAAAAGGC
CAATTGCGGCATATTTATACAACGGGTAAATACAGAAGTAGTTAAATATTTTAAATTTTT
TTTTAAAGAGCCAACAGCACCACCGTTGACACCTCAAAATATGGGATTCATTGTTCAACA
ACAACCACATTTTCCTATTCCGCCACCACCATATCCAACGAATTTTACGAATGATCCTTC
ATCAAATTCACTGCCCTATCCAGGATCGAATTCACTGCCTTATCCTCAATCGAATTCACT
ACCCTATCCTCCATCGGATGCACTGCCTTATCCTTCATCAAATTCTTTGCCATATCCTTC
ATTTAATCCACAATCAACAGACGTCCAAACAACTCAACCAACAGCCAATACAACAAATAC
GATTATAGTTCAACCACCACAGCTTGGATCTGATCCAGTCGTATGTTACTGTCCAAACTG
TAATGAGAATGTGACTACAAAAGTCGATTATAAAGCTGGCACTCAAACACACTTGTCTGC
TGCTCTTCTTTGTGCATTAAATGATGATTGTTGTTGTGCCTTGCTTCCATATTGCTGCAA
TTGTACTAAAGATGCTCACCATTATTGCCCAAAGTGTAATCACTATTTTGGAAAAAGTCA
ACCATTTGGTTAATCATGAATTTAGTTTATGAAGCTTTTCAAAGGAATAAACGAATAGTT
TTCAAGTGCAATTAATAATTTTTTAAGTAGTGTGAGCTCGAATGCATTAAATTAAAAATC
GATATATTTGTTAATTAAAGTAATTCAGTTGAATGCACTGGACATGAACAAGCAAAAATG
TACATAATTTTTGAAATTAATAAATTTGATATTGCTTAATGAATCATTTGTTGAATGATA
ATGGAACATAGAATAAAATATTACAAACCATTAAGGCCATTAATTGATAATTAATGTTTT
AATATATACCACTGCAAAAACAGCAACAAATGCGAAAGAAGAAAAAAATTGGAAAATGCC
AGCTCTCTCTCAGCTTGGTAATATAAAAAACGCGAAATTTA

>g5606.t2 Gene=g5606 Length=170
MGFIVQQQPHFPIPPPPYPTNFTNDPSSNSLPYPGSNSLPYPQSNSLPYPPSDALPYPSS
NSLPYPSFNPQSTDVQTTQPTANTTNTIIVQPPQLGSDPVVCYCPNCNENVTTKVDYKAG
TQTHLSAALLCALNDDCCCALLPYCCNCTKDAHHYCPKCNHYFGKSQPFG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g5606.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 46 -
6 g5606.t2 MobiDBLite mobidb-lite consensus disorder prediction 23 43 -
2 g5606.t2 PANTHER PTHR23292:SF14 FI16615P1-RELATED 39 164 4.3E-24
3 g5606.t2 PANTHER PTHR23292 LIPOPOLYSACCHARIDE-INDUCED TUMOR NECROSIS FACTOR-ALPHA FACTOR 39 164 4.3E-24
1 g5606.t2 Pfam PF10601 LITAF-like zinc ribbon domain 98 165 1.0E-19
7 g5606.t2 ProSiteProfiles PS51837 LITAF domain profile. 84 168 17.796
4 g5606.t2 SMART SM00714 litaf 99 168 1.8E-12

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5606/g5606.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5606.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