General information for g5679.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5679 is located on chr_2: 11229194..11230624 (- strand)
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 | g5679 | g5679.t2 | TTS | g5679.t2 | 11229135 | 11229135 |
| chr_2 | g5679 | g5679.t2 | isoform | g5679.t2 | 11229194 | 11230624 |
| chr_2 | g5679 | g5679.t2 | exon | g5679.t2.exon1 | 11229194 | 11230523 |
| chr_2 | g5679 | g5679.t2 | cds | g5679.t2.CDS1 | 11229878 | 11230523 |
| chr_2 | g5679 | g5679.t2 | exon | g5679.t2.exon2 | 11230581 | 11230624 |
| chr_2 | g5679 | g5679.t2 | cds | g5679.t2.CDS2 | 11230581 | 11230624 |
| chr_2 | g5679 | g5679.t2 | TSS | g5679.t2 | 11230648 | 11230648 |
Sequences
>g5679.t2 Gene=g5679 Length=1374
ATGGACGAAAAATTAATAAATAAAACGTTTTCTTCATTAAATCTTTTAGATATGGATTTC
TCTGAGTTGGAAGATGTCACAATTTCATTAACTAAAAAATTCATTCAAAATTTAATGAAT
TTTAAAGATACCACAATAAGTGAAGAAACTTTCAAAGAAATATCACTAAATTGTATCAAA
CATTTGAAAGTTAGTTGCACAAAAGGACCATCATTTCAAAATCTAATAATCAACACAAAT
GGTATGCTTGAATCACTAAAAGAAATGTTGAAGAATGAAGAAAAGAAATTCGATAATGTT
AAAACAAAGGTTTTTGAATTGATAGCAAATTTGTGTGTCAAGAATGAAAAGTGTCAAAAA
AAGATTTGGAATGAAGTGAATGAGTTGATCATTTGTGAATTAACATCATCTAATGTGCAA
AATGTCAATATAAGTGCTATGATTATTTATAACATAAAGATTGGAATAAATGAGAATATT
GAAATTGAACAAGCCTTGAATGTTGCTCTCGATCATTATGATAATTTTTTGAAGAACAAT
ATTTCTATGCCAGATTTTCTACATATTCTACTTGATTATTTCATATGCTCATGTGATGTT
GTTCAATCATATAAAAAACTTACCTCTGAAAAACAACGTATCTTTCTTTATTATGTCAAT
GATTATATAGAAAATGAATCTAATCAGTAAGTCTAATATTGAAGGTATATTAAATATTTA
AATTTTAATTTGAATCTTTTTAGAATTATAAACACATCACTTCTGAAACATCTAACATTT
GAATTCAAAAAAAAATCTGATTGTGTACTGAAAACTGTGACTTCTTACGTTGATTCAATT
GATCCAGAGGTTGTAGTTACATTGCTTGATATAATCTCAACTGCAACTGCACAGGATAAA
TATTTGAGCTTATTGCGTGATGATGCATCGCTTTTTCTCAACATTGGTTGTTTGCTTCAA
GCCCTCCATAAAATTGGCAAAGAATCAAAAAACACATTTAGTCCTATTCAAAATCTTGAA
GCATTAATACCAAATGCCAATGATAATGCTGATTTTGAAAAAGAAATCTCATTTTCATTC
AAGACTAAACTTGTAAAATCATTAGCAAATCTTTCATATCGCAATAAGAGAAATCAGGAA
TTAGCAAGAGAAATGGAAATTATGCAGAGCATTTTTGAGTGTACTAATGCAGATGCTAGA
AATCCTCTTATTAAAGAGTGGAGTATTTTAGCAATTCGTAATTTATGTGAAGAAAACAGT
GAAAATCAAGACATTGTACAGAGTTTAACACGAATCGGAGATGCACAAAATCCTGTACTT
ACCGAATTCGGATTGTCTGAAGGTGTTTTTAGAATTAAAAAACATAACATGTGA
>g5679.t2 Gene=g5679 Length=229
MDEKLINKTFSSLNLLDMDFSELEDVTISLTKKFIQNLMNFKDTTISEETFKEISLNCIK
HLKVSCTKGPSFQNLIINTNGMLESLKEMLKNEEKKFDNVKTKVFELIANLCVKNEKCQK
KIWNEVNELIICELTSSNVQNVNISAMIIYNIKIGINENIEIEQALNVALDHYDNFLKNN
ISMPDFLHILLDYFICSCDVVQSYKKLTSEKQRIFLYYVNDYIENESNQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5679.t2 | Coils | Coil | Coil | 76 | 103 | - |
| 1 | g5679.t2 | SUPERFAMILY | SSF48371 | ARM repeat | 52 | 163 | 1.62E-7 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5679/g5679.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5679.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.
