General information for g5788.t50
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein disulfide-isomerase.
Parent gene
- The parent gene g5788 is located on chr_2: 11943105..11945282 (- 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 | g5788 | g5788.t50 | TTS | g5788.t50 | 11940782 | 11940782 |
| chr_2 | g5788 | g5788.t50 | isoform | g5788.t50 | 11941386 | 11943292 |
| chr_2 | g5788 | g5788.t50 | exon | g5788.t50.exon1 | 11941386 | 11942487 |
| chr_2 | g5788 | g5788.t50 | cds | g5788.t50.CDS1 | 11941387 | 11941968 |
| chr_2 | g5788 | g5788.t50 | exon | g5788.t50.exon2 | 11943148 | 11943292 |
| chr_2 | g5788 | g5788.t50 | TSS | g5788.t50 | 11943390 | 11943390 |
Sequences
>g5788.t50 Gene=g5788 Length=1247
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTGCACTTGCTCCAGAATACGCAAAAGCTGCAAAGAT
TTTGGCTGAAAAGGAATCAAATGTCAAATTAGGCAAAGTTGATGCCACAGAGGAATCAGA
TTTAGCAGAGGAGTTCCAGGTTCGCGGTTATCCAACACTCAAGTTCTTCCGCAATGGTTC
ACCAATTGAATATAATGGAGGACGACAGGCTGATGATATTGTCTCATGGCTTTTGAAAAA
AACTGGCCCAGCTGCTAAAGAATTGGATTCAGTTGAAACTGCTGAGGCTTTGTTGAAAGA
CAATCAAGTCGTTGTTGTTGGTTTCTTCAGCGATCGCGAATCAGATAATTTCAAAGCATT
CTTGGCTGCTGCTAATGCTGTTGATGATTATCCATTTGCCATCACAAACAATGCTGATGT
TCTTAAGAAATACGAGGCTAAAGATGGAAAAATTGTTCTCTTCAAACAATTCGATGAAGG
CAAAGCTGTTTTTGACGGAACATTTGATGAAGCTTCAATCAAGAAATTTGTCCAAAGTCA
AGCTATGCCATTGGTAGTCGATTTCAATCATGAATCAGCACAAAAGATTTTCGGTGGTGA
TATCAAATCACACTTGCTCATGTTCTTGTCAAAGGAAGCCGGACACTTTGAAAAATATGT
TGATGCCGCTAAGGAAATTGCAAAAGACTTTAGAGAAAAGATTCTCTTTGTTTCAATTAA
CGCTGATGAAGAAGACCACAACCGTATTTTGGAATTCTTCGGTATGAAGAAAGACGAAGT
TCCATCAATGAGAATCATTCAATTGCAAGAAGATATGGCTAAATTCAAGCCAGAAAAAGC
CGATTTGAGCGCTGATGCTATTAAAGACTTTGTTCAAAAGTTCTTGGATGGAAAATTGAA
GCAACACTTGCTTAGTCAAGAATTACCAGAAGATTGGGATAAGAATCCAGTTAAAGTTTT
GGTTTCAACCAATTTCGATGAAGTGGCCTTCGATAAGACAAAGGATGTTCTAGTTGAATT
CTATGCTCCCTGGTGCTCGCATTGCAAGCAACTTGCTCCAATCTACGATCAATTGGCCGA
GAAATTCAAGGATAATGATGCTATTGTTATTGCCAAGATGGATGCTA
>g5788.t50 Gene=g5788 Length=194
MPLVVDFNHESAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINA
DEEDHNRILEFFGMKKDEVPSMRIIQLQEDMAKFKPEKADLSADAIKDFVQKFLDGKLKQ
HLLSQELPEDWDKNPVKVLVSTNFDEVAFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEK
FKDNDAIVIAKMDA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5788.t50 | CDD | cd02982 | PDI_b’_family | 11 | 114 | 0.00 |
| 7 | g5788.t50 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 1 | 128 | 0.00 |
| 8 | g5788.t50 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 129 | 194 | 0.00 |
| 3 | g5788.t50 | PANTHER | PTHR18929:SF101 | PROTEIN DISULFIDE-ISOMERASE | 1 | 194 | 0.00 |
| 4 | g5788.t50 | PANTHER | PTHR18929 | PROTEIN DISULFIDE ISOMERASE | 1 | 194 | 0.00 |
| 1 | g5788.t50 | Pfam | PF13848 | Thioredoxin-like domain | 1 | 112 | 0.00 |
| 2 | g5788.t50 | Pfam | PF00085 | Thioredoxin | 136 | 194 | 0.00 |
| 9 | g5788.t50 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 100 | 194 | 11.35 |
| 6 | g5788.t50 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 1 | 132 | 0.00 |
| 5 | g5788.t50 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 134 | 194 | 0.00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5788/g5788.t50; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t50.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.
