General information for g5788.t27
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.t27 | TTS | g5788.t27 | 11940782 | 11940782 |
| chr_2 | g5788 | g5788.t27 | isoform | g5788.t27 | 11940804 | 11943292 |
| chr_2 | g5788 | g5788.t27 | exon | g5788.t27.exon1 | 11940804 | 11941158 |
| chr_2 | g5788 | g5788.t27 | cds | g5788.t27.CDS1 | 11941105 | 11941158 |
| chr_2 | g5788 | g5788.t27 | exon | g5788.t27.exon2 | 11941219 | 11942487 |
| chr_2 | g5788 | g5788.t27 | cds | g5788.t27.CDS2 | 11941219 | 11942487 |
| chr_2 | g5788 | g5788.t27 | exon | g5788.t27.exon3 | 11943119 | 11943292 |
| chr_2 | g5788 | g5788.t27 | cds | g5788.t27.CDS3 | 11943119 | 11943292 |
| chr_2 | g5788 | g5788.t27 | TSS | g5788.t27 | 11943390 | 11943390 |
Sequences
>g5788.t27 Gene=g5788 Length=1798
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTGTAAGTATTACATAGACCAATTGTTTATTGCACTT
GCTCCAGAATACGCAAAAGCTGCAAAGATTTTGGCTGAAAAGGAATCAAATGTCAAATTA
GGCAAAGTTGATGCCACAGAGGAATCAGATTTAGCAGAGGAGTTCCAGGTTCGCGGTTAT
CCAACACTCAAGTTCTTCCGCAATGGTTCACCAATTGAATATAATGGAGGACGACAGGCT
GATGATATTGTCTCATGGCTTTTGAAAAAAACTGGCCCAGCTGCTAAAGAATTGGATTCA
GTTGAAACTGCTGAGGCTTTGTTGAAAGACAATCAAGTCGTTGTTGTTGGTTTCTTCAGC
GATCGCGAATCAGATAATTTCAAAGCATTCTTGGCTGCTGCTAATGCTGTTGATGATTAT
CCATTTGCCATCACAAACAATGCTGATGTTCTTAAGAAATACGAGGCTAAAGATGGAAAA
ATTGTTCTCTTCAAACAATTCGATGAAGGCAAAGCTGTTTTTGACGGAACATTTGATGAA
GCTTCAATCAAGAAATTTGTCCAAAGTCAAGCTATGCCATTGGTAGTCGATTTCAATCAT
GAATCAGCACAAAAGATTTTCGGTGGTGATATCAAATCACACTTGCTCATGTTCTTGTCA
AAGGAAGCCGGACACTTTGAAAAATATGTTGATGCCGCTAAGGAAATTGCAAAAGACTTT
AGAGAAAAGATTCTCTTTGTTTCAATTAACGCTGATGAAGAAGACCACAACCGTATTTTG
GAATTCTTCGGTATGAAGAAAGACGAAGTTCCATCAATGAGAATCATTCAATTGCAAGAA
GATATGGCTAAATTCAAGCCAGAAAAAGCCGATTTGAGCGCTGATGCTATTAAAGACTTT
GTTCAAAAGTTCTTGGATGGAAAATTGAAGCAACACTTGCTTAGTCAAGAATTACCAGAA
GATTGGGATAAGAATCCAGTTAAAGTTTTGGTTTCAACCAATTTCGATGAAGTGGCCTTC
GATAAGACAAAGGATGTTCTAGTTGAATTCTATGCTCCCTGGTGCTCGCATTGCAAGCAA
CTTGCTCCAATCTACGATCAATTGGCCGAGAAATTCAAGGATAATGATGCTATTGTTATT
GCCAAGATGGATGCTACTGTAAATGAGCTAGAACATACAAAGATTCAATCCTTCCCAACA
CTCAAATTGTACAAAAAGGGTGATAACTCAGTTGTAGATTTTAATGGTGAACGCACACTT
GAAGGATTATCGAAATTCCTTGAATCAGGTGGCTTAGAAGATGCTGCTGGTGTACCAGAT
GTTGAGGAAGTACCTGTTGATGAGGATGATGATGCATCAAGAAAAGATGAACTGTAAATA
AGATGATCCCTTCTTCCTTTACTTAAGTTTTAGAAATCTTTTTTTATTAGTATCATTTTC
TTTCACAAAAAAAATCCATTGTTGTCAGTACATTCTCTGCTAAGTTGATATGCTCAAAAA
AAGATATAGTAAAAAGATAAAATACTTTAAACCGATCTCTTAATACAGAGAGATGATTAA
TGAAGCATTTCCGCATCATTTGTTCATTTATTTCTCGATAAGGTGTGCGTGCATATGAGA
AGATTTAATTCCAAAACATTTTTTTATCGAAAACAAAAAAATTGAAATAAAATACATA
>g5788.t27 Gene=g5788 Length=498
MKWILLLSSLLILNLIHASEIKEEEGVLVLTKSNFKEALKNEFILVEFCKYYIDQLFIAL
APEYAKAAKILAEKESNVKLGKVDATEESDLAEEFQVRGYPTLKFFRNGSPIEYNGGRQA
DDIVSWLLKKTGPAAKELDSVETAEALLKDNQVVVVGFFSDRESDNFKAFLAAANAVDDY
PFAITNNADVLKKYEAKDGKIVLFKQFDEGKAVFDGTFDEASIKKFVQSQAMPLVVDFNH
ESAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINADEEDHNRIL
EFFGMKKDEVPSMRIIQLQEDMAKFKPEKADLSADAIKDFVQKFLDGKLKQHLLSQELPE
DWDKNPVKVLVSTNFDEVAFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEKFKDNDAIVI
AKMDATVNELEHTKIQSFPTLKLYKKGDNSVVDFNGERTLEGLSKFLESGGLEDAAGVPD
VEEVPVDEDDDASRKDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g5788.t27 | CDD | cd02961 | PDI_a_family | 28 | 127 | 3.47024E-28 |
| 23 | g5788.t27 | CDD | cd02981 | PDI_b_family | 135 | 229 | 2.88355E-23 |
| 24 | g5788.t27 | CDD | cd02982 | PDI_b’_family | 242 | 345 | 1.50264E-19 |
| 26 | g5788.t27 | CDD | cd02995 | PDI_a_PDI_a’_C | 366 | 467 | 8.71113E-50 |
| 17 | g5788.t27 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 15 | 130 | 1.2E-30 |
| 16 | g5788.t27 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 131 | 231 | 2.3E-33 |
| 14 | g5788.t27 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 232 | 359 | 3.4E-46 |
| 15 | g5788.t27 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 360 | 472 | 1.1E-40 |
| 28 | g5788.t27 | MobiDBLite | mobidb-lite | consensus disorder prediction | 474 | 498 | - |
| 29 | g5788.t27 | MobiDBLite | mobidb-lite | consensus disorder prediction | 480 | 498 | - |
| 4 | g5788.t27 | PANTHER | PTHR18929:SF101 | PROTEIN DISULFIDE-ISOMERASE | 7 | 492 | 6.9E-180 |
| 5 | g5788.t27 | PANTHER | PTHR18929 | PROTEIN DISULFIDE ISOMERASE | 7 | 492 | 6.9E-180 |
| 7 | g5788.t27 | PRINTS | PR00421 | Thioredoxin family signature | 386 | 394 | 1.0E-6 |
| 6 | g5788.t27 | PRINTS | PR00421 | Thioredoxin family signature | 394 | 403 | 1.0E-6 |
| 8 | g5788.t27 | PRINTS | PR00421 | Thioredoxin family signature | 434 | 445 | 1.0E-6 |
| 2 | g5788.t27 | Pfam | PF00085 | Thioredoxin | 27 | 127 | 4.8E-17 |
| 1 | g5788.t27 | Pfam | PF13848 | Thioredoxin-like domain | 159 | 343 | 4.8E-36 |
| 3 | g5788.t27 | Pfam | PF00085 | Thioredoxin | 367 | 468 | 6.2E-27 |
| 19 | g5788.t27 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 20 | g5788.t27 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 21 | g5788.t27 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 22 | g5788.t27 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 18 | g5788.t27 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 498 | - |
| 32 | g5788.t27 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 10 | 132 | 8.954 |
| 33 | g5788.t27 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 331 | 472 | 15.573 |
| 9 | g5788.t27 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 25 | 133 | 7.38E-26 |
| 11 | g5788.t27 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 136 | 233 | 1.88E-24 |
| 10 | g5788.t27 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 231 | 363 | 6.99E-26 |
| 12 | g5788.t27 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 365 | 469 | 4.41E-32 |
| 13 | g5788.t27 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 27 | g5788.t27 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 30 | g5788.t27 | TIGRFAM | TIGR01130 | ER_PDI_fam: protein disulfide isomerase | 26 | 498 | 1.2E-142 |
| 31 | g5788.t27 | TIGRFAM | TIGR01126 | pdi_dom: protein disulfide-isomerase domain | 370 | 468 | 4.4E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5788/g5788.t27; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t27.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. There were no conditions that were differentially expressed