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.t39 TTS g5788.t39 11940782 11940782
chr_2 g5788 g5788.t39 isoform g5788.t39 11941105 11943292
chr_2 g5788 g5788.t39 exon g5788.t39.exon1 11941105 11941158
chr_2 g5788 g5788.t39 cds g5788.t39.CDS1 11941105 11941158
chr_2 g5788 g5788.t39 exon g5788.t39.exon2 11941219 11942168
chr_2 g5788 g5788.t39 cds g5788.t39.CDS2 11941219 11941968
chr_2 g5788 g5788.t39 exon g5788.t39.exon3 11942416 11942487
chr_2 g5788 g5788.t39 exon g5788.t39.exon4 11943144 11943292
chr_2 g5788 g5788.t39 TSS g5788.t39 11943390 11943390

Sequences

>g5788.t39 Gene=g5788 Length=1225
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTGTAAGCACTTGCTCCAGAATACGCAAAAGCTGCAA
AGATTTTGGCTGAAAAGGAATCAAATGTCAAATTAGGCAAAATAATTTCAAAGCATTCTT
GGCTGCTGCTAATGCTGTTGATGATTATCCATTTGCCATCACAAACAATGCTGATGTTCT
TAAGAAATACGAGGCTAAAGATGGAAAAATTGTTCTCTTCAAACAATTCGATGAAGGCAA
AGCTGTTTTTGACGGAACATTTGATGAAGCTTCAATCAAGAAATTTGTCCAAAGTCAAGC
TATGCCATTGGTAGTCGATTTCAATCATGAATCAGCACAAAAGATTTTCGGTGGTGATAT
CAAATCACACTTGCTCATGTTCTTGTCAAAGGAAGCCGGACACTTTGAAAAATATGTTGA
TGCCGCTAAGGAAATTGCAAAAGACTTTAGAGAAAAGATTCTCTTTGTTTCAATTAACGC
TGATGAAGAAGACCACAACCGTATTTTGGAATTCTTCGGTATGAAGAAAGACGAAGTTCC
ATCAATGAGAATCATTCAATTGCAAGAAGATATGGCTAAATTCAAGCCAGAAAAAGCCGA
TTTGAGCGCTGATGCTATTAAAGACTTTGTTCAAAAGTTCTTGGATGGAAAATTGAAGCA
ACACTTGCTTAGTCAAGAATTACCAGAAGATTGGGATAAGAATCCAGTTAAAGTTTTGGT
TTCAACCAATTTCGATGAAGTGGCCTTCGATAAGACAAAGGATGTTCTAGTTGAATTCTA
TGCTCCCTGGTGCTCGCATTGCAAGCAACTTGCTCCAATCTACGATCAATTGGCCGAGAA
ATTCAAGGATAATGATGCTATTGTTATTGCCAAGATGGATGCTACTGTAAATGAGCTAGA
ACATACAAAGATTCAATCCTTCCCAACACTCAAATTGTACAAAAAGGGTGATAACTCAGT
TGTAGATTTTAATGGTGAACGCACACTTGAAGGATTATCGAAATTCCTTGAATCAGGTGG
CTTAGAAGATGCTGCTGGTGTACCAGATGTTGAGGAAGTACCTGTTGATGAGGATGATGA
TGCATCAAGAAAAGATGAACTGTAA

>g5788.t39 Gene=g5788 Length=267
MPLVVDFNHESAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINA
DEEDHNRILEFFGMKKDEVPSMRIIQLQEDMAKFKPEKADLSADAIKDFVQKFLDGKLKQ
HLLSQELPEDWDKNPVKVLVSTNFDEVAFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEK
FKDNDAIVIAKMDATVNELEHTKIQSFPTLKLYKKGDNSVVDFNGERTLEGLSKFLESGG
LEDAAGVPDVEEVPVDEDDDASRKDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5788.t39 CDD cd02982 PDI_b’_family 11 114 1.31681E-20
13 g5788.t39 CDD cd02995 PDI_a_PDI_a’_C 135 236 3.06254E-52
10 g5788.t39 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 128 1.2E-46
11 g5788.t39 Gene3D G3DSA:3.40.30.10 Glutaredoxin 129 241 3.1E-41
14 g5788.t39 MobiDBLite mobidb-lite consensus disorder prediction 243 267 -
15 g5788.t39 MobiDBLite mobidb-lite consensus disorder prediction 249 267 -
3 g5788.t39 PANTHER PTHR18929:SF101 PROTEIN DISULFIDE-ISOMERASE 1 261 4.1E-102
4 g5788.t39 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 1 261 4.1E-102
6 g5788.t39 PRINTS PR00421 Thioredoxin family signature 155 163 2.1E-7
7 g5788.t39 PRINTS PR00421 Thioredoxin family signature 163 172 2.1E-7
5 g5788.t39 PRINTS PR00421 Thioredoxin family signature 203 214 2.1E-7
1 g5788.t39 Pfam PF13848 Thioredoxin-like domain 1 112 6.6E-20
2 g5788.t39 Pfam PF00085 Thioredoxin 136 237 1.9E-27
17 g5788.t39 ProSiteProfiles PS51352 Thioredoxin domain profile. 100 241 15.573
9 g5788.t39 SUPERFAMILY SSF52833 Thioredoxin-like 1 132 4.48E-26
8 g5788.t39 SUPERFAMILY SSF52833 Thioredoxin-like 134 238 1.39E-32
16 g5788.t39 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.t39; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t39.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.

Raw TPM values