General information for g5788.t38
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.t38 | TTS | g5788.t38 | 11940782 | 11940782 |
| chr_2 | g5788 | g5788.t38 | isoform | g5788.t38 | 11941105 | 11943292 |
| chr_2 | g5788 | g5788.t38 | exon | g5788.t38.exon1 | 11941105 | 11941158 |
| chr_2 | g5788 | g5788.t38 | cds | g5788.t38.CDS1 | 11941105 | 11941158 |
| chr_2 | g5788 | g5788.t38 | exon | g5788.t38.exon2 | 11941231 | 11942487 |
| chr_2 | g5788 | g5788.t38 | cds | g5788.t38.CDS2 | 11941231 | 11941968 |
| chr_2 | g5788 | g5788.t38 | exon | g5788.t38.exon3 | 11943144 | 11943292 |
| chr_2 | g5788 | g5788.t38 | TSS | g5788.t38 | 11943390 | 11943390 |
Sequences
>g5788.t38 Gene=g5788 Length=1460
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTGTAAGCACTTGCTCCAGAATACGCAAAAGCTGCAA
AGATTTTGGCTGAAAAGGAATCAAATGTCAAATTAGGCAAAGTTGATGCCACAGAGGAAT
CAGATTTAGCAGAGGAGTTCCAGGTTCGCGGTTATCCAACACTCAAGTTCTTCCGCAATG
GTTCACCAATTGAATATAATGGAGGACGACAGGCTGATGATATTGTCTCATGGCTTTTGA
AAAAAACTGGCCCAGCTGCTAAAGAATTGGATTCAGTTGAAACTGCTGAGGCTTTGTTGA
AAGACAATCAAGTCGTTGTTGTTGGTTTCTTCAGCGATCGCGAATCAGATAATTTCAAAG
CATTCTTGGCTGCTGCTAATGCTGTTGATGATTATCCATTTGCCATCACAAACAATGCTG
ATGTTCTTAAGAAATACGAGGCTAAAGATGGAAAAATTGTTCTCTTCAAACAATTCGATG
AAGGCAAAGCTGTTTTTGACGGAACATTTGATGAAGCTTCAATCAAGAAATTTGTCCAAA
GTCAAGCTATGCCATTGGTAGTCGATTTCAATCATGAATCAGCACAAAAGATTTTCGGTG
GTGATATCAAATCACACTTGCTCATGTTCTTGTCAAAGGAAGCCGGACACTTTGAAAAAT
ATGTTGATGCCGCTAAGGAAATTGCAAAAGACTTTAGAGAAAAGATTCTCTTTGTTTCAA
TTAACGCTGATGAAGAAGACCACAACCGTATTTTGGAATTCTTCGGTATGAAGAAAGACG
AAGTTCCATCAATGAGAATCATTCAATTGCAAGAAGATATGGCTAAATTCAAGCCAGAAA
AAGCCGATTTGAGCGCTGATGCTATTAAAGACTTTGTTCAAAAGTTCTTGGATGGAAAAT
TGAAGCAACACTTGCTTAGTCAAGAATTACCAGAAGATTGGGATAAGAATCCAGTTAAAG
TTTTGGTTTCAACCAATTTCGATGAAGTGGCCTTCGATAAGACAAAGGATGTTCTAGTTG
AATTCTATGCTCCCTGGTGCTCGCATTGCAAGCAACTTGCTCCAATCTACGATCAATTGG
CCGAGAAATTCAAGGATAATGATGCTATTGTTATTGCCAAGATGGATGCTACTGTAAATG
AGCTAGAACATACAAAGATTCAATCCTTCCCAACACTCAAATTGTACAAAAAGGGTGATA
ACTCAGTTGTAGATTTTAATGGTGAACGCACACTTGAAGGATTATCGAAATTCCTTGAAT
CAGGTGGCTTAGAAGATGCTGCTGGTGAGGAAGTACCTGTTGATGAGGATGATGATGCAT
CAAGAAAAGATGAACTGTAA
>g5788.t38 Gene=g5788 Length=263
MPLVVDFNHESAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINA
DEEDHNRILEFFGMKKDEVPSMRIIQLQEDMAKFKPEKADLSADAIKDFVQKFLDGKLKQ
HLLSQELPEDWDKNPVKVLVSTNFDEVAFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEK
FKDNDAIVIAKMDATVNELEHTKIQSFPTLKLYKKGDNSVVDFNGERTLEGLSKFLESGG
LEDAAGEEVPVDEDDDASRKDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5788.t38 | CDD | cd02982 | PDI_b’_family | 11 | 114 | 1.37231E-20 |
| 13 | g5788.t38 | CDD | cd02995 | PDI_a_PDI_a’_C | 135 | 236 | 1.67352E-52 |
| 10 | g5788.t38 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 1 | 128 | 1.1E-46 |
| 11 | g5788.t38 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 129 | 241 | 3.0E-41 |
| 15 | g5788.t38 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 263 | - |
| 14 | g5788.t38 | MobiDBLite | mobidb-lite | consensus disorder prediction | 246 | 263 | - |
| 3 | g5788.t38 | PANTHER | PTHR18929:SF101 | PROTEIN DISULFIDE-ISOMERASE | 1 | 261 | 1.0E-101 |
| 4 | g5788.t38 | PANTHER | PTHR18929 | PROTEIN DISULFIDE ISOMERASE | 1 | 261 | 1.0E-101 |
| 6 | g5788.t38 | PRINTS | PR00421 | Thioredoxin family signature | 155 | 163 | 2.0E-7 |
| 7 | g5788.t38 | PRINTS | PR00421 | Thioredoxin family signature | 163 | 172 | 2.0E-7 |
| 5 | g5788.t38 | PRINTS | PR00421 | Thioredoxin family signature | 203 | 214 | 2.0E-7 |
| 1 | g5788.t38 | Pfam | PF13848 | Thioredoxin-like domain | 1 | 112 | 6.4E-20 |
| 2 | g5788.t38 | Pfam | PF00085 | Thioredoxin | 136 | 237 | 1.8E-27 |
| 17 | g5788.t38 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 100 | 241 | 15.573 |
| 9 | g5788.t38 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 1 | 132 | 4.23E-26 |
| 8 | g5788.t38 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 134 | 238 | 1.34E-32 |
| 16 | g5788.t38 | TIGRFAM | TIGR01126 | pdi_dom: protein disulfide-isomerase domain | 139 | 237 | 1.3E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5788/g5788.t38; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t38.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003756 | protein disulfide isomerase activity | MF |
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.
