Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein disulfide-isomerase.

Parent gene

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.t34 TTS g5788.t34 11940782 11940782
chr_2 g5788 g5788.t34 isoform g5788.t34 11940804 11943292
chr_2 g5788 g5788.t34 exon g5788.t34.exon1 11940804 11941158
chr_2 g5788 g5788.t34 cds g5788.t34.CDS1 11941105 11941158
chr_2 g5788 g5788.t34 exon g5788.t34.exon2 11941219 11941597
chr_2 g5788 g5788.t34 cds g5788.t34.CDS2 11941219 11941597
chr_2 g5788 g5788.t34 exon g5788.t34.exon3 11941679 11942487
chr_2 g5788 g5788.t34 cds g5788.t34.CDS3 11941679 11941968
chr_2 g5788 g5788.t34 exon g5788.t34.exon4 11943144 11943292
chr_2 g5788 g5788.t34 TSS g5788.t34 11943390 11943390

Sequences

>g5788.t34 Gene=g5788 Length=1692
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTGTAAGCACTTGCTCCAGAATACGCAAAAGCTGCAA
AGATTTTGGCTGAAAAGGAATCAAATGTCAAATTAGGCAAAGTTGATGCCACAGAGGAAT
CAGATTTAGCAGAGGAGTTCCAGGTTCGCGGTTATCCAACACTCAAGTTCTTCCGCAATG
GTTCACCAATTGAATATAATGGAGGACGACAGGCTGATGATATTGTCTCATGGCTTTTGA
AAAAAACTGGCCCAGCTGCTAAAGAATTGGATTCAGTTGAAACTGCTGAGGCTTTGTTGA
AAGACAATCAAGTCGTTGTTGTTGGTTTCTTCAGCGATCGCGAATCAGATAATTTCAAAG
CATTCTTGGCTGCTGCTAATGCTGTTGATGATTATCCATTTGCCATCACAAACAATGCTG
ATGTTCTTAAGAAATACGAGGCTAAAGATGGAAAAATTGTTCTCTTCAAACAATTCGATG
AAGGCAAAGCTGTTTTTGACGGAACATTTGATGAAGCTTCAATCAAGAAATTTGTCCAAA
GTCAAGCTATGCCATTGGTAGTCGATTTCAATCATGAATCAGCACAAAAGATTTTCGGTG
GTGATATCAAATCACACTTGCTCATGTTCTTGTCAAAGGAAGCCGGACACTTTGAAAAAT
ATGTTGATGCCGCTAAGGAAATTGCAAAAGACTTTAGAGAAAAGATTCTCTTTGTTTCAA
TTAACGCTGATGAAGAAGACCACAACCGTATTTTGGAATTCTTCGGTATGAAGAAAGACG
AAGTTCCATCAATGAGAATCATTCAATTGCAAGAAGATATGGCTAAATTCAAGCCAGATC
AAGAATTACCAGAAGATTGGGATAAGAATCCAGTTAAAGTTTTGGTTTCAACCAATTTCG
ATGAAGTGGCCTTCGATAAGACAAAGGATGTTCTAGTTGAATTCTATGCTCCCTGGTGCT
CGCATTGCAAGCAACTTGCTCCAATCTACGATCAATTGGCCGAGAAATTCAAGGATAATG
ATGCTATTGTTATTGCCAAGATGGATGCTACTGTAAATGAGCTAGAACATACAAAGATTC
AATCCTTCCCAACACTCAAATTGTACAAAAAGGGTGATAACTCAGTTGTAGATTTTAATG
GTGAACGCACACTTGAAGGATTATCGAAATTCCTTGAATCAGGTGGCTTAGAAGATGCTG
CTGGTGTACCAGATGTTGAGGAAGTACCTGTTGATGAGGATGATGATGCATCAAGAAAAG
ATGAACTGTAAATAAGATGATCCCTTCTTCCTTTACTTAAGTTTTAGAAATCTTTTTTTA
TTAGTATCATTTTCTTTCACAAAAAAAATCCATTGTTGTCAGTACATTCTCTGCTAAGTT
GATATGCTCAAAAAAAGATATAGTAAAAAGATAAAATACTTTAAACCGATCTCTTAATAC
AGAGAGATGATTAATGAAGCATTTCCGCATCATTTGTTCATTTATTTCTCGATAAGGTGT
GCGTGCATATGAGAAGATTTAATTCCAAAACATTTTTTTATCGAAAACAAAAAAATTGAA
ATAAAATACATA

>g5788.t34 Gene=g5788 Length=240
MPLVVDFNHESAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINA
DEEDHNRILEFFGMKKDEVPSMRIIQLQEDMAKFKPDQELPEDWDKNPVKVLVSTNFDEV
AFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEKFKDNDAIVIAKMDATVNELEHTKIQSF
PTLKLYKKGDNSVVDFNGERTLEGLSKFLESGGLEDAAGVPDVEEVPVDEDDDASRKDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g5788.t34 CDD cd02982 PDI_b’_family 11 99 5.08274E-15
15 g5788.t34 CDD cd02995 PDI_a_PDI_a’_C 108 209 1.56352E-52
13 g5788.t34 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 106 5.4E-29
12 g5788.t34 Gene3D G3DSA:3.40.30.10 Glutaredoxin 107 214 1.9E-32
17 g5788.t34 MobiDBLite mobidb-lite consensus disorder prediction 216 240 -
16 g5788.t34 MobiDBLite mobidb-lite consensus disorder prediction 222 240 -
4 g5788.t34 PANTHER PTHR18929:SF101 PROTEIN DISULFIDE-ISOMERASE 1 99 1.8E-83
6 g5788.t34 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 1 99 1.8E-83
3 g5788.t34 PANTHER PTHR18929:SF101 PROTEIN DISULFIDE-ISOMERASE 98 234 1.8E-83
5 g5788.t34 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 98 234 1.8E-83
8 g5788.t34 PRINTS PR00421 Thioredoxin family signature 128 136 1.6E-7
7 g5788.t34 PRINTS PR00421 Thioredoxin family signature 136 145 1.6E-7
9 g5788.t34 PRINTS PR00421 Thioredoxin family signature 176 187 1.6E-7
1 g5788.t34 Pfam PF13848 Thioredoxin-like domain 1 101 5.6E-17
2 g5788.t34 Pfam PF00085 Thioredoxin 109 210 1.5E-27
19 g5788.t34 ProSiteProfiles PS51352 Thioredoxin domain profile. 89 214 15.699
11 g5788.t34 SUPERFAMILY SSF52833 Thioredoxin-like 1 100 4.1E-16
10 g5788.t34 SUPERFAMILY SSF52833 Thioredoxin-like 107 211 1.08E-32
18 g5788.t34 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 112 210 1.1E-34

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5788/g5788.t34; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t34.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