General information for g5788.t1
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.t1 | TTS | g5788.t1 | 11940782 | 11940782 |
| chr_2 | g5788 | g5788.t1 | isoform | g5788.t1 | 11941105 | 11943292 |
| chr_2 | g5788 | g5788.t1 | exon | g5788.t1.exon1 | 11941105 | 11941158 |
| chr_2 | g5788 | g5788.t1 | cds | g5788.t1.CDS1 | 11941105 | 11941158 |
| chr_2 | g5788 | g5788.t1 | exon | g5788.t1.exon2 | 11941219 | 11942487 |
| chr_2 | g5788 | g5788.t1 | cds | g5788.t1.CDS2 | 11941219 | 11942487 |
| chr_2 | g5788 | g5788.t1 | exon | g5788.t1.exon3 | 11942552 | 11942561 |
| chr_2 | g5788 | g5788.t1 | cds | g5788.t1.CDS3 | 11942552 | 11942561 |
| chr_2 | g5788 | g5788.t1 | exon | g5788.t1.exon4 | 11942788 | 11942803 |
| chr_2 | g5788 | g5788.t1 | cds | g5788.t1.CDS4 | 11942788 | 11942803 |
| chr_2 | g5788 | g5788.t1 | exon | g5788.t1.exon5 | 11943148 | 11943292 |
| chr_2 | g5788 | g5788.t1 | cds | g5788.t1.CDS5 | 11943148 | 11943292 |
| chr_2 | g5788 | g5788.t1 | TSS | g5788.t1 | 11943390 | 11943390 |
Sequences
>g5788.t1 Gene=g5788 Length=1494
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTATGCACCATGGTGTGGACATTGTAAGGCACTTGCT
CCAGAATACGCAAAAGCTGCAAAGATTTTGGCTGAAAAGGAATCAAATGTCAAATTAGGC
AAAGTTGATGCCACAGAGGAATCAGATTTAGCAGAGGAGTTCCAGGTTCGCGGTTATCCA
ACACTCAAGTTCTTCCGCAATGGTTCACCAATTGAATATAATGGAGGACGACAGGCTGAT
GATATTGTCTCATGGCTTTTGAAAAAAACTGGCCCAGCTGCTAAAGAATTGGATTCAGTT
GAAACTGCTGAGGCTTTGTTGAAAGACAATCAAGTCGTTGTTGTTGGTTTCTTCAGCGAT
CGCGAATCAGATAATTTCAAAGCATTCTTGGCTGCTGCTAATGCTGTTGATGATTATCCA
TTTGCCATCACAAACAATGCTGATGTTCTTAAGAAATACGAGGCTAAAGATGGAAAAATT
GTTCTCTTCAAACAATTCGATGAAGGCAAAGCTGTTTTTGACGGAACATTTGATGAAGCT
TCAATCAAGAAATTTGTCCAAAGTCAAGCTATGCCATTGGTAGTCGATTTCAATCATGAA
TCAGCACAAAAGATTTTCGGTGGTGATATCAAATCACACTTGCTCATGTTCTTGTCAAAG
GAAGCCGGACACTTTGAAAAATATGTTGATGCCGCTAAGGAAATTGCAAAAGACTTTAGA
GAAAAGATTCTCTTTGTTTCAATTAACGCTGATGAAGAAGACCACAACCGTATTTTGGAA
TTCTTCGGTATGAAGAAAGACGAAGTTCCATCAATGAGAATCATTCAATTGCAAGAAGAT
ATGGCTAAATTCAAGCCAGAAAAAGCCGATTTGAGCGCTGATGCTATTAAAGACTTTGTT
CAAAAGTTCTTGGATGGAAAATTGAAGCAACACTTGCTTAGTCAAGAATTACCAGAAGAT
TGGGATAAGAATCCAGTTAAAGTTTTGGTTTCAACCAATTTCGATGAAGTGGCCTTCGAT
AAGACAAAGGATGTTCTAGTTGAATTCTATGCTCCCTGGTGCTCGCATTGCAAGCAACTT
GCTCCAATCTACGATCAATTGGCCGAGAAATTCAAGGATAATGATGCTATTGTTATTGCC
AAGATGGATGCTACTGTAAATGAGCTAGAACATACAAAGATTCAATCCTTCCCAACACTC
AAATTGTACAAAAAGGGTGATAACTCAGTTGTAGATTTTAATGGTGAACGCACACTTGAA
GGATTATCGAAATTCCTTGAATCAGGTGGCTTAGAAGATGCTGCTGGTGTACCAGATGTT
GAGGAAGTACCTGTTGATGAGGATGATGATGCATCAAGAAAAGATGAACTGTAA
>g5788.t1 Gene=g5788 Length=497
MKWILLLSSLLILNLIHASEIKEEEGVLVLTKSNFKEALKNEFILVEFYAPWCGHCKALA
PEYAKAAKILAEKESNVKLGKVDATEESDLAEEFQVRGYPTLKFFRNGSPIEYNGGRQAD
DIVSWLLKKTGPAAKELDSVETAEALLKDNQVVVVGFFSDRESDNFKAFLAAANAVDDYP
FAITNNADVLKKYEAKDGKIVLFKQFDEGKAVFDGTFDEASIKKFVQSQAMPLVVDFNHE
SAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINADEEDHNRILE
FFGMKKDEVPSMRIIQLQEDMAKFKPEKADLSADAIKDFVQKFLDGKLKQHLLSQELPED
WDKNPVKVLVSTNFDEVAFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEKFKDNDAIVIA
KMDATVNELEHTKIQSFPTLKLYKKGDNSVVDFNGERTLEGLSKFLESGGLEDAAGVPDV
EEVPVDEDDDASRKDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g5788.t1 | CDD | cd02961 | PDI_a_family | 28 | 126 | 4.13457E-42 |
| 23 | g5788.t1 | CDD | cd02981 | PDI_b_family | 134 | 228 | 1.20249E-23 |
| 24 | g5788.t1 | CDD | cd02982 | PDI_b’_family | 241 | 344 | 6.45438E-20 |
| 26 | g5788.t1 | CDD | cd02995 | PDI_a_PDI_a’_C | 365 | 466 | 4.63861E-50 |
| 15 | g5788.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 15 | 129 | 1.9E-41 |
| 14 | g5788.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 130 | 230 | 2.2E-33 |
| 17 | g5788.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 231 | 358 | 3.2E-46 |
| 16 | g5788.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 359 | 471 | 1.1E-40 |
| 29 | g5788.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 473 | 497 | - |
| 30 | g5788.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 479 | 497 | - |
| 4 | g5788.t1 | PANTHER | PTHR18929:SF101 | PROTEIN DISULFIDE-ISOMERASE | 7 | 491 | 6.4E-192 |
| 5 | g5788.t1 | PANTHER | PTHR18929 | PROTEIN DISULFIDE ISOMERASE | 7 | 491 | 6.4E-192 |
| 7 | g5788.t1 | PRINTS | PR00421 | Thioredoxin family signature | 44 | 52 | 4.9E-8 |
| 6 | g5788.t1 | PRINTS | PR00421 | Thioredoxin family signature | 52 | 61 | 4.9E-8 |
| 8 | g5788.t1 | PRINTS | PR00421 | Thioredoxin family signature | 95 | 106 | 4.9E-8 |
| 3 | g5788.t1 | Pfam | PF00085 | Thioredoxin | 27 | 126 | 7.8E-32 |
| 1 | g5788.t1 | Pfam | PF13848 | Thioredoxin-like domain | 158 | 342 | 4.9E-36 |
| 2 | g5788.t1 | Pfam | PF00085 | Thioredoxin | 366 | 467 | 6.2E-27 |
| 19 | g5788.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 20 | g5788.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 21 | g5788.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 13 | - |
| 22 | g5788.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 18 | g5788.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 497 | - |
| 28 | g5788.t1 | ProSitePatterns | PS00194 | Thioredoxin family active site. | 45 | 63 | - |
| 35 | g5788.t1 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 10 | 131 | 15.076 |
| 34 | g5788.t1 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 330 | 471 | 15.573 |
| 12 | g5788.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 25 | 132 | 1.09E-37 |
| 11 | g5788.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 135 | 232 | 1.88E-24 |
| 9 | g5788.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 230 | 362 | 6.99E-26 |
| 10 | g5788.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 364 | 468 | 4.46E-32 |
| 13 | g5788.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 27 | g5788.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 31 | g5788.t1 | TIGRFAM | TIGR01130 | ER_PDI_fam: protein disulfide isomerase | 26 | 497 | 7.8E-161 |
| 32 | g5788.t1 | TIGRFAM | TIGR01126 | pdi_dom: protein disulfide-isomerase domain | 30 | 129 | 3.8E-38 |
| 33 | g5788.t1 | TIGRFAM | TIGR01126 | pdi_dom: protein disulfide-isomerase domain | 369 | 467 | 4.3E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5788/g5788.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003756 | protein disulfide isomerase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09580 (protein disulfide-isomerase A1)
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.
