Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein disulfide-isomerase A3.

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_1 g10334 g10334.t9 TTS g10334.t9 8933125 8933125
chr_1 g10334 g10334.t9 isoform g10334.t9 8933413 8934833
chr_1 g10334 g10334.t9 exon g10334.t9.exon1 8933413 8933710
chr_1 g10334 g10334.t9 cds g10334.t9.CDS1 8933413 8933710
chr_1 g10334 g10334.t9 exon g10334.t9.exon2 8933766 8933942
chr_1 g10334 g10334.t9 cds g10334.t9.CDS2 8933766 8933942
chr_1 g10334 g10334.t9 exon g10334.t9.exon3 8934000 8934407
chr_1 g10334 g10334.t9 cds g10334.t9.CDS3 8934000 8934407
chr_1 g10334 g10334.t9 exon g10334.t9.exon4 8934468 8934696
chr_1 g10334 g10334.t9 cds g10334.t9.CDS4 8934468 8934696
chr_1 g10334 g10334.t9 exon g10334.t9.exon5 8934755 8934833
chr_1 g10334 g10334.t9 cds g10334.t9.CDS5 8934755 8934776
chr_1 g10334 g10334.t9 TSS g10334.t9 8935652 8935652

Sequences

>g10334.t9 Gene=g10334 Length=1191
TTTCTGGATATCCCACTCTCAAAATTTTCAGAAACGGTGAAAATCCTCAGGATTATAATG
GTCCACGTGAAGCAAGTAAGTGGTATTGTGAAATATATGAGAGCACAAGTTGGTCCATCA
TCAAAGGATCTTCTAACAGTTGAAGCATATGAAAAGTTCTTGGGTGTTCAAGAGGGTGCC
GTAGTTGGATTCTTTGAAAAAGAAACGGATTTGAAGACTGTTTTCTTAAAATATGCCGAT
TTGCAACGTGAGAAACTTCGCTTTGCACATTCAAGTGATCCAGAAATTCTCAAGAAAGTT
GGCGAAACAAACGCTATTCTTCTTTATCGTGCACCACAATTGAGTAATAAGTTTGAACCA
TCTTTTGTTAAATTCACTGGAAAAGATTCAAGTGATCTTAAAGAATTTGTTAAGAAGAAC
TTCCACGGTTTAGTTGGTGTACGTAGTCGTGATACTATTACTGATTTCAACAATCCATTG
GTAACTGCATATTATGCTGTTGATTATATTAAAAATGCAAAAGGCACAAACTACTGGCGC
AATCGTGTACTTAAAGTTGCCAAAGAATGGGAAGGTAAAATCAATTTTGCTATTGCTGCT
AAAGATGAATTCCAACATGAATTGAATGAATATGGTTACGATTATGTCGGTGATAAACCA
ATAATTTTGGCTCGTGACGCTCAAAATCAAAAGTTCATCATGAAAGATGAGTTTTCTGTT
GACAATCTTCAAGCATTTGTCAATGATCTTTATGAAGGCAATCTGGAGCCTTACGTTAAA
TCAGAAGCAATTCCAGTCGATCAAGATGGCCCAGTTACAGTTGTAGTTGCAAAGAACTTT
AATGAGGCTGTTCCAAAAGATAAGGATGTTTTAATCGAATTCTACGCACCATGGTGTGGT
CATTGCAAAAAATTAGCTCCAACATTCGATGAATTAGGAACAAAATTGAAGGGTGAAGAT
GTTGTTATTGCCAAAATGGATGCTACTGCAAACGATGTTCCTCCTCAATTTGATGTTCGC
GGATTCCCGACACTCTTCTGGTTGCCTAAGGGCGCTCATGATAAACCAGTTAGATACGAT
GGCGGTCGTGAATTGAACGATTTTATCAGCTACATCAGTAAACACGCTACAAATGAATTA
AAAGGATACGATCGCTCTGGAAACGAAAAGAAACAAAAGACAGAATTGTAA

>g10334.t9 Gene=g10334 Length=377
MVHVKQVSGIVKYMRAQVGPSSKDLLTVEAYEKFLGVQEGAVVGFFEKETDLKTVFLKYA
DLQREKLRFAHSSDPEILKKVGETNAILLYRAPQLSNKFEPSFVKFTGKDSSDLKEFVKK
NFHGLVGVRSRDTITDFNNPLVTAYYAVDYIKNAKGTNYWRNRVLKVAKEWEGKINFAIA
AKDEFQHELNEYGYDYVGDKPIILARDAQNQKFIMKDEFSVDNLQAFVNDLYEGNLEPYV
KSEAIPVDQDGPVTVVVAKNFNEAVPKDKDVLIEFYAPWCGHCKKLAPTFDELGTKLKGE
DVVIAKMDATANDVPPQFDVRGFPTLFWLPKGAHDKPVRYDGGRELNDFISYISKHATNE
LKGYDRSGNEKKQKTEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g10334.t9 CDD cd03073 PDI_b’_ERp72_ERp57 126 231 2.79598E-38
15 g10334.t9 CDD cd02995 PDI_a_PDI_a’_C 252 353 1.47929E-50
11 g10334.t9 Gene3D G3DSA:3.40.30.10 Glutaredoxin 16 128 1.8E-30
13 g10334.t9 Gene3D G3DSA:3.40.30.10 Glutaredoxin 131 234 1.2E-34
12 g10334.t9 Gene3D G3DSA:3.40.30.10 Glutaredoxin 240 376 1.2E-40
3 g10334.t9 PANTHER PTHR18929:SF60 PROTEIN DISULFIDE-ISOMERASE 6 361 9.2E-108
4 g10334.t9 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 6 361 9.2E-108
7 g10334.t9 PRINTS PR00421 Thioredoxin family signature 271 279 4.1E-6
5 g10334.t9 PRINTS PR00421 Thioredoxin family signature 279 288 4.1E-6
6 g10334.t9 PRINTS PR00421 Thioredoxin family signature 319 330 4.1E-6
1 g10334.t9 Pfam PF13848 Thioredoxin-like domain 47 230 2.0E-32
2 g10334.t9 Pfam PF00085 Thioredoxin 253 354 8.3E-28
16 g10334.t9 ProSitePatterns PS00194 Thioredoxin family active site. 272 290 -
19 g10334.t9 ProSiteProfiles PS51352 Thioredoxin domain profile. 231 358 15.679
10 g10334.t9 SUPERFAMILY SSF52833 Thioredoxin-like 23 122 5.72E-12
8 g10334.t9 SUPERFAMILY SSF52833 Thioredoxin-like 124 250 6.04E-17
9 g10334.t9 SUPERFAMILY SSF52833 Thioredoxin-like 217 357 2.57E-33
17 g10334.t9 TIGRFAM TIGR01130 ER_PDI_fam: protein disulfide isomerase 7 376 7.4E-106
18 g10334.t9 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 256 356 1.2E-34

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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