General information for g5647.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5647 is located on chr_2: 10882166..10884280 (+ 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 | g5647 | g5647.t28 | TSS | g5647.t28 | 10879963 | 10879963 |
| chr_2 | g5647 | g5647.t28 | isoform | g5647.t28 | 10880028 | 10881127 |
| chr_2 | g5647 | g5647.t28 | exon | g5647.t28.exon1 | 10880028 | 10880085 |
| chr_2 | g5647 | g5647.t28 | exon | g5647.t28.exon2 | 10880608 | 10881127 |
| chr_2 | g5647 | g5647.t28 | cds | g5647.t28.CDS1 | 10880642 | 10881127 |
| chr_2 | g5647 | g5647.t28 | TTS | g5647.t28 | 10880810 | 10880810 |
Sequences
>g5647.t28 Gene=g5647 Length=578
CCAAAGTTGAATTTTTTGAAAAATAATTCGATTGAAAAATTTATGAAAGTACAATAAAAT
AATAGATAAACCAAAGTTCTGACTTTCTAAAAATGAATATGAACAAGGGTGATAATAAAG
AGAAAATGGGAGGAAAATTGACTCATGTTGAATTAGAAAGTACTGAAGGTGGAAAAGAAA
AGTTGACTCATGTTGAAATACAAGGCACTGGAGGTGGAAAAGGAAGTGATGAAAAGTGTC
CAGAAATGAAAGGTGATGTTCAAAAAACAAGCTCTGAAAGCAAAATTCAAGGTCATTCTG
GTATGATGCAAGGAATGAAAGGTGGCTCACAAGGAAAATGTCCAACAAGAGAATGCAAGG
AATTAAAAGGAAAAGTTGAGAAAGCTAGCTCAGAACATAAGGATAAGAATCAAGCTCATT
CCGAATTTATGAAAGAAATGGAGAAAAAAGGAAACAATGGAAAATGTCCAGCTCGTGATT
GTCCTAAAATGAAGGAAAAGTTTCAAAAATTAAGCTCTGACATGATGGGCAAGGATAAAG
CTCATTCTGATATCAAAGAAGAAATGAATAAAGGAAAA
>g5647.t28 Gene=g5647 Length=162
MNMNKGDNKEKMGGKLTHVELESTEGGKEKLTHVEIQGTGGGKGSDEKCPEMKGDVQKTS
SESKIQGHSGMMQGMKGGSQGKCPTRECKELKGKVEKASSEHKDKNQAHSEFMKEMEKKG
NNGKCPARDCPKMKEKFQKLSSDMMGKDKAHSDIKEEMNKGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5647.t28 | Coils | Coil | Coil | 88 | 108 | - |
| 2 | g5647.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 22 | 67 | - |
| 1 | g5647.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 162 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5647/g5647.t28; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5647.t28.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.
