General information for g5616.t1
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.t1 | TTS | g5616.t1 | 10644702 | 10644702 |
| chr_2 | g5616 | g5616.t1 | isoform | g5616.t1 | 10644770 | 10645327 |
| chr_2 | g5616 | g5616.t1 | exon | g5616.t1.exon1 | 10644770 | 10644983 |
| chr_2 | g5616 | g5616.t1 | cds | g5616.t1.CDS1 | 10644770 | 10644983 |
| chr_2 | g5616 | g5616.t1 | exon | g5616.t1.exon2 | 10645046 | 10645182 |
| chr_2 | g5616 | g5616.t1 | cds | g5616.t1.CDS2 | 10645046 | 10645182 |
| chr_2 | g5616 | g5616.t1 | exon | g5616.t1.exon3 | 10645250 | 10645327 |
| chr_2 | g5616 | g5616.t1 | cds | g5616.t1.CDS3 | 10645250 | 10645327 |
| chr_2 | g5616 | g5616.t1 | TSS | g5616.t1 | 10645434 | 10645434 |
Sequences
>g5616.t1 Gene=g5616 Length=429
ATGTCTTATATGCTTACACATCTTCACAATGGATGGCAAGTTGATCAAGCGATTTTAAGT
GAAGAAGATAGAATTGTGGTAATTCGCTTTGGACATGATTGGGATCCAACTTGCATGAAA
ATGGATGAAGTACTCTACAACATTGCCGAAAAAGTGAAAAATTTTGCAGTCATTTATTTA
GTCGATATCACAGAAGTTCCAGATTTCAACAAAATGTATGAATTGTATGATCCTTGTACC
GTAATGTTCTTCTTTAGAAATAAACACATTATGATTGATCTGGGAACGGGTAATAATAAC
AAAATTAATTGGGCTCTAGAAGATGTTCAAGAGATGATTGATATAGTAGAGACAGTTTAT
AGAGGCGCAAGAAAAGGACGTGGTTTGGTTGTGTCACCTAAAGATTATTCTACAAAATAC
CGCTATTAA
>g5616.t1 Gene=g5616 Length=142
MSYMLTHLHNGWQVDQAILSEEDRIVVIRFGHDWDPTCMKMDEVLYNIAEKVKNFAVIYL
VDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWALEDVQEMIDIVETVY
RGARKGRGLVVSPKDYSTKYRY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5616.t1 | CDD | cd02954 | DIM1 | 10 | 123 | 0 |
| 6 | g5616.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 1 | 141 | 0 |
| 2 | g5616.t1 | PANTHER | PTHR12052:SF9 | - | 1 | 142 | 0 |
| 3 | g5616.t1 | PANTHER | PTHR12052 | THIOREDOXIN-LIKE PROTEN 4A, 4B | 1 | 142 | 0 |
| 7 | g5616.t1 | PIRSF | PIRSF017199 | Dim1 | 1 | 142 | 0 |
| 1 | g5616.t1 | Pfam | PF02966 | Mitosis protein DIM1 | 4 | 136 | 0 |
| 5 | g5616.t1 | SMART | SM01410 | DIM1_2 | 4 | 136 | 0 |
| 4 | g5616.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 3 | 137 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5616/g5616.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5616.t1.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 transcript has been annotated with K12859 (U5 snRNP protein, DIM1 family)
Pathway
- This transcript belongs to the following pathways
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.
