General information for g5641.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5641 is located on chr_2: 10813609..10820834 (+ 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 | g5641 | g5641.t3 | TSS | g5641.t3 | 10812977 | 10812977 |
| chr_2 | g5641 | g5641.t3 | isoform | g5641.t3 | 10813609 | 10814996 |
| chr_2 | g5641 | g5641.t3 | exon | g5641.t3.exon1 | 10813609 | 10813765 |
| chr_2 | g5641 | g5641.t3 | cds | g5641.t3.CDS1 | 10813609 | 10813765 |
| chr_2 | g5641 | g5641.t3 | exon | g5641.t3.exon2 | 10814081 | 10814996 |
| chr_2 | g5641 | g5641.t3 | cds | g5641.t3.CDS2 | 10814081 | 10814430 |
| chr_2 | g5641 | g5641.t3 | TTS | g5641.t3 | NA | NA |
Sequences
>g5641.t3 Gene=g5641 Length=1073
ATGGGACAATCTTCAAGCATTCTTCAGCAGTCATCATCGCTAAAAAGAAGATTCTTTCTT
GTTACACCCAAAAAATTGATCAGGCTACGTAGACAAACATCATGCGAAAATTCAGGAGCT
GTATCGAGCCATCAAAATGAATTTACGCAAGCGCTAAATGAAAATGTTGAGACAGCAAAG
CACAACCACGATGACAAAGTGGCAGCAACGTTCAGTCGTGATCCAACAGCGCGAGACGAG
AGTTTGATTGAAGAAAATTTATTGCAACAGTTGCGTGAATTAATTGAAAATTTATTGTGC
GGCGGAGATCGAATTGATGGCGATATTGTACTTGAGATTGATACAATTGAGAAAACTTTA
AAAATTTTACCACAGCAAACGAGTTCATTGGTCAAGGAAGATCAGGAAGGTAATTATTTT
TTATTATGTGTAACTCTTTCGTTTTGGCTGTCTTTCTTTCTCTTTCTTTCATTCATTTTT
GCTCATTCTATGATTTGTTCTATATAATACGTGTACACTTTTTTCATGCCTCTCTTTCTT
TTCTCAATTCTTTTTACTTATTTCTCGAGAGTTGAGAGATCAGCGATCGATTTAAATGGT
CAAAAACCAGTTTTTAGTGAAAAAAGAAATGGGATAGATACGAAACACGGGAAAAACACA
CATATTTCTTAAATGGTTCACAATTATTTGTTTTTATTTGATTAAAAACGTGATATTATA
TCACTCGTGAGAAAAAATAATAAAATCTATTATGCCATTTTGAGCCCTTTTAGGTATTTT
ATATTTTAATCAAAATTATGGAAATGAGATGAACGAAAAAATGAGCAAGAGAGACAGACT
CGCGATGTAAAAAGTGAAAACAGTGAATATCAATATAAATTTCTTTATAATAATATGATA
TTATATTTTTGTGTCGCTGAGTGATGATGCAAGTTTTCTCCCGAAAAAATGTGTCGATTA
TGAAATTTGTTAAATAATGAATTTTCTCTCATCTTTTTTTCTTCTTTTCTATGAATTTTT
TTATCAACTATCAACTGTTTATTTTCCGTTCGTCACATGCGTACAAAAAAAGA
>g5641.t3 Gene=g5641 Length=168
MGQSSSILQQSSSLKRRFFLVTPKKLIRLRRQTSCENSGAVSSHQNEFTQALNENVETAK
HNHDDKVAATFSRDPTARDESLIEENLLQQLRELIENLLCGGDRIDGDIVLEIDTIEKTL
KILPQQTSSLVKEDQEGNYFLLCVTLSFWLSFFLFLSFIFAHSMICSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5641.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 138 | - |
| 4 | g5641.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 161 | - |
| 2 | g5641.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 162 | 168 | - |
| 1 | g5641.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 161 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5641/g5641.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5641.t3.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.
