General information for g5483.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5483 is located on chr_2: 9835346..9836011 (+ 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 | g5483 | g5483.t13 | isoform | g5483.t13 | 9834708 | 9836011 |
| chr_2 | g5483 | g5483.t13 | exon | g5483.t13.exon1 | 9834708 | 9834876 |
| chr_2 | g5483 | g5483.t13 | exon | g5483.t13.exon2 | 9834938 | 9835050 |
| chr_2 | g5483 | g5483.t13 | exon | g5483.t13.exon3 | 9835107 | 9836011 |
| chr_2 | g5483 | g5483.t13 | cds | g5483.t13.CDS1 | 9835161 | 9835346 |
| chr_2 | g5483 | g5483.t13 | TSS | g5483.t13 | 9835302 | 9835302 |
| chr_2 | g5483 | g5483.t13 | TTS | g5483.t13 | 9836018 | 9836018 |
Sequences
>g5483.t13 Gene=g5483 Length=1187
GTTTCAAAAAGAGTTCGTGAATGGGATGTTGGAAAGAAAGAAGATTTAGAGCATGATGAA
AGCAGAGAAAGGCGTCGTCGAAGATCTTCAGAACGAGAAAATCGTCGAGAGAAGGAGCGA
AAACAATTGGAAGAGTCTACTGTAGAGAGACGACATAGTGTTACACCTGGACGAGAAGAT
AAAGATGCAATTCCATCACAGCCTGGTCGTTTATTAGATGATTTGTTCCGGAAATCTAAA
GCTGTTCCATGCATTTATTGGCTACCACTTTCTGAAGAACAGATCAAAGAGAAGGAAGAA
CAACGACAAAAAAATATTGCTGAACATAATCGTCGCATGGAAGAAATAATAAAAAATAGG
GAATTACAGCGTGAGAAAATGAATGAAGAAAGACGCGAACGCGAAGCAAAGCGTCGTGAG
GAGAGAAAAGATCGCGAAAGAAAGCGTACAAGATCACGTAGCCGTAGTGTTCGTCGTTAT
TCGCGTGAGAGACATCGTGATCGACGATACGATCGTCGATAAATTTGTATTTTACTCTCA
TCCTTTTTCACAGCTTGTCAAAAAAAAATTAATAATTATATTAATTGCACTCATTTGTAA
CTATACAAGTTTATGGTTGCATTTTTAAATTTTTAAGAGTGCTTTTTACTTCAACTACTA
TTTCAATAACATCAAAATTTAAGTTCAAGTGATTGTTTTCATATTTCAATATTGGATCAA
ATTTGATTCTAAAATTCTTAATACTTTTTCTTTTTCTAACCATATCCATTTTTCCTTTTA
AAATTTTCTGTCCCTCATCAAGACTATTACATACCATACACACAAAATTTTGGTTCTGTT
TGCTTTTTCTTCTTTTCTTCTATATACCAGAGTTTAAATTAGAATATAAGTGTTTAAACC
GAGAAACAGGACGAAAATTGAGAGAGAGAGACGAAGTAATGTTGTCGACTACAATATTGA
GAAAAGGATTCAATGTGAAACTTATGCAAAAAAAATTATCAGTGAAATGGATCGTTTACG
AAGATAACTAATACTAAATAATATATGCCACCTAGTGTAGTAAAACACGCTCGTGTTCAT
CGTGGGAGTTGATCGAAATTTGAATCATCAGATTATGAATCACAACTTAAAATGAATATG
TGCGGTTTATGAATTTAAATTTTTCTTCTTATTAAATAAAACTAAAT
>g5483.t13 Gene=g5483 Length=61
MEEIIKNRELQREKMNEERREREAKRREERKDRERKRTRSRSRSVRRYSRERHRDRRYDR
R
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g5483.t13 | Coils | Coil | Coil | 1 | 35 | - |
| 1 | g5483.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 61 | - |
| 3 | g5483.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 2 | g5483.t13 | MobiDBLite | mobidb-lite | consensus disorder prediction | 36 | 55 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5483/g5483.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5483.t13.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.
