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.t11 TTS g5788.t11 11940782 11940782
chr_2 g5788 g5788.t11 isoform g5788.t11 11940804 11943292
chr_2 g5788 g5788.t11 exon g5788.t11.exon1 11940804 11941158
chr_2 g5788 g5788.t11 cds g5788.t11.CDS1 11941105 11941158
chr_2 g5788 g5788.t11 exon g5788.t11.exon2 11941219 11942500
chr_2 g5788 g5788.t11 cds g5788.t11.CDS2 11941219 11941968
chr_2 g5788 g5788.t11 exon g5788.t11.exon3 11943148 11943292
chr_2 g5788 g5788.t11 TSS g5788.t11 11943390 11943390

Sequences

>g5788.t11 Gene=g5788 Length=1782
ATGAAGTGGATATTACTACTTTCAAGTCTTTTAATTCTAAATTTAATTCACGCAAGTGAA
ATTAAAGAGGAAGAAGGTGTTTTAGTCTTGACAAAATCAAATTTCAAAGAGGCACTTAAG
AATGAATTCATTTTAGTTGAATTTTTTTGCACAAATAGGCACTTGCTCCAGAATACGCAA
AAGCTGCAAAGATTTTGGCTGAAAAGGAATCAAATGTCAAATTAGGCAAAGTTGATGCCA
CAGAGGAATCAGATTTAGCAGAGGAGTTCCAGGTTCGCGGTTATCCAACACTCAAGTTCT
TCCGCAATGGTTCACCAATTGAATATAATGGAGGACGACAGGCTGATGATATTGTCTCAT
GGCTTTTGAAAAAAACTGGCCCAGCTGCTAAAGAATTGGATTCAGTTGAAACTGCTGAGG
CTTTGTTGAAAGACAATCAAGTCGTTGTTGTTGGTTTCTTCAGCGATCGCGAATCAGATA
ATTTCAAAGCATTCTTGGCTGCTGCTAATGCTGTTGATGATTATCCATTTGCCATCACAA
ACAATGCTGATGTTCTTAAGAAATACGAGGCTAAAGATGGAAAAATTGTTCTCTTCAAAC
AATTCGATGAAGGCAAAGCTGTTTTTGACGGAACATTTGATGAAGCTTCAATCAAGAAAT
TTGTCCAAAGTCAAGCTATGCCATTGGTAGTCGATTTCAATCATGAATCAGCACAAAAGA
TTTTCGGTGGTGATATCAAATCACACTTGCTCATGTTCTTGTCAAAGGAAGCCGGACACT
TTGAAAAATATGTTGATGCCGCTAAGGAAATTGCAAAAGACTTTAGAGAAAAGATTCTCT
TTGTTTCAATTAACGCTGATGAAGAAGACCACAACCGTATTTTGGAATTCTTCGGTATGA
AGAAAGACGAAGTTCCATCAATGAGAATCATTCAATTGCAAGAAGATATGGCTAAATTCA
AGCCAGAAAAAGCCGATTTGAGCGCTGATGCTATTAAAGACTTTGTTCAAAAGTTCTTGG
ATGGAAAATTGAAGCAACACTTGCTTAGTCAAGAATTACCAGAAGATTGGGATAAGAATC
CAGTTAAAGTTTTGGTTTCAACCAATTTCGATGAAGTGGCCTTCGATAAGACAAAGGATG
TTCTAGTTGAATTCTATGCTCCCTGGTGCTCGCATTGCAAGCAACTTGCTCCAATCTACG
ATCAATTGGCCGAGAAATTCAAGGATAATGATGCTATTGTTATTGCCAAGATGGATGCTA
CTGTAAATGAGCTAGAACATACAAAGATTCAATCCTTCCCAACACTCAAATTGTACAAAA
AGGGTGATAACTCAGTTGTAGATTTTAATGGTGAACGCACACTTGAAGGATTATCGAAAT
TCCTTGAATCAGGTGGCTTAGAAGATGCTGCTGGTGTACCAGATGTTGAGGAAGTACCTG
TTGATGAGGATGATGATGCATCAAGAAAAGATGAACTGTAAATAAGATGATCCCTTCTTC
CTTTACTTAAGTTTTAGAAATCTTTTTTTATTAGTATCATTTTCTTTCACAAAAAAAATC
CATTGTTGTCAGTACATTCTCTGCTAAGTTGATATGCTCAAAAAAAGATATAGTAAAAAG
ATAAAATACTTTAAACCGATCTCTTAATACAGAGAGATGATTAATGAAGCATTTCCGCAT
CATTTGTTCATTTATTTCTCGATAAGGTGTGCGTGCATATGAGAAGATTTAATTCCAAAA
CATTTTTTTATCGAAAACAAAAAAATTGAAATAAAATACATA

>g5788.t11 Gene=g5788 Length=267
MPLVVDFNHESAQKIFGGDIKSHLLMFLSKEAGHFEKYVDAAKEIAKDFREKILFVSINA
DEEDHNRILEFFGMKKDEVPSMRIIQLQEDMAKFKPEKADLSADAIKDFVQKFLDGKLKQ
HLLSQELPEDWDKNPVKVLVSTNFDEVAFDKTKDVLVEFYAPWCSHCKQLAPIYDQLAEK
FKDNDAIVIAKMDATVNELEHTKIQSFPTLKLYKKGDNSVVDFNGERTLEGLSKFLESGG
LEDAAGVPDVEEVPVDEDDDASRKDEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5788.t11 CDD cd02982 PDI_b’_family 11 114 1.31681E-20
13 g5788.t11 CDD cd02995 PDI_a_PDI_a’_C 135 236 3.06254E-52
10 g5788.t11 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 128 1.2E-46
11 g5788.t11 Gene3D G3DSA:3.40.30.10 Glutaredoxin 129 241 3.1E-41
14 g5788.t11 MobiDBLite mobidb-lite consensus disorder prediction 243 267 -
15 g5788.t11 MobiDBLite mobidb-lite consensus disorder prediction 249 267 -
3 g5788.t11 PANTHER PTHR18929:SF101 PROTEIN DISULFIDE-ISOMERASE 1 261 4.1E-102
4 g5788.t11 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 1 261 4.1E-102
6 g5788.t11 PRINTS PR00421 Thioredoxin family signature 155 163 2.1E-7
7 g5788.t11 PRINTS PR00421 Thioredoxin family signature 163 172 2.1E-7
5 g5788.t11 PRINTS PR00421 Thioredoxin family signature 203 214 2.1E-7
1 g5788.t11 Pfam PF13848 Thioredoxin-like domain 1 112 6.6E-20
2 g5788.t11 Pfam PF00085 Thioredoxin 136 237 1.9E-27
17 g5788.t11 ProSiteProfiles PS51352 Thioredoxin domain profile. 100 241 15.573
9 g5788.t11 SUPERFAMILY SSF52833 Thioredoxin-like 1 132 4.48E-26
8 g5788.t11 SUPERFAMILY SSF52833 Thioredoxin-like 134 238 1.39E-32
16 g5788.t11 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.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5788.t11.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