General information for g5616.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Thioredoxin-like protein 4A.
Parent gene
- The parent gene g5616 is located on chr_2: 10644770..10645327 (- 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 | g5616 | g5616.t2 | TTS | g5616.t2 | 10644702 | 10644702 |
| chr_2 | g5616 | g5616.t2 | isoform | g5616.t2 | 10644770 | 10645327 |
| chr_2 | g5616 | g5616.t2 | exon | g5616.t2.exon1 | 10644770 | 10644983 |
| chr_2 | g5616 | g5616.t2 | cds | g5616.t2.CDS1 | 10644770 | 10644983 |
| chr_2 | g5616 | g5616.t2 | exon | g5616.t2.exon2 | 10645046 | 10645327 |
| chr_2 | g5616 | g5616.t2 | cds | g5616.t2.CDS2 | 10645046 | 10645140 |
| chr_2 | g5616 | g5616.t2 | TSS | g5616.t2 | 10645434 | 10645434 |
Sequences
>g5616.t2 Gene=g5616 Length=496
ATGTCTTATATGCTTACACATCTTCACAATGGATGGCAAGTTGATCAAGCGATTTTAAGT
GAAGAAGATAGAATTGTGGTAAGTTGATTGCTTTTTTCGTTTTTAATCGTAAACATTTTT
TGAGATAAAATCTTCTTTTATAAAGGTAATTCGCTTTGGACATGATTGGGATCCAACTTG
CATGAAAATGGATGAAGTACTCTACAACATTGCCGAAAAAGTGAAAAATTTTGCAGTCAT
TTATTTAGTCGATATCACAGAAGTTCCAGATTTCAACAAAATGTATGAATTGTATGATCC
TTGTACCGTAATGTTCTTCTTTAGAAATAAACACATTATGATTGATCTGGGAACGGGTAA
TAATAACAAAATTAATTGGGCTCTAGAAGATGTTCAAGAGATGATTGATATAGTAGAGAC
AGTTTATAGAGGCGCAAGAAAAGGACGTGGTTTGGTTGTGTCACCTAAAGATTATTCTAC
AAAATACCGCTATTAA
>g5616.t2 Gene=g5616 Length=102
MDEVLYNIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNN
KINWALEDVQEMIDIVETVYRGARKGRGLVVSPKDYSTKYRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5616.t2 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 1 | 102 | 0 |
| 2 | g5616.t2 | PANTHER | PTHR12052:SF9 | - | 1 | 102 | 0 |
| 3 | g5616.t2 | PANTHER | PTHR12052 | THIOREDOXIN-LIKE PROTEN 4A, 4B | 1 | 102 | 0 |
| 7 | g5616.t2 | PIRSF | PIRSF017199 | Dim1 | 1 | 102 | 0 |
| 1 | g5616.t2 | Pfam | PF02966 | Mitosis protein DIM1 | 1 | 96 | 0 |
| 5 | g5616.t2 | SMART | SM01410 | DIM1_2 | 1 | 96 | 0 |
| 4 | g5616.t2 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 1 | 97 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5616/g5616.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5616.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0000398 | mRNA splicing, via spliceosome | BP |
| GO:0046540 | U4/U6 x U5 tri-snRNP complex | CC |
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