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.t12 TTS g10334.t12 8933125 8933125
chr_1 g10334 g10334.t12 isoform g10334.t12 8933413 8935088
chr_1 g10334 g10334.t12 exon g10334.t12.exon1 8933413 8933710
chr_1 g10334 g10334.t12 cds g10334.t12.CDS1 8933413 8933710
chr_1 g10334 g10334.t12 exon g10334.t12.exon2 8933766 8933942
chr_1 g10334 g10334.t12 cds g10334.t12.CDS2 8933766 8933942
chr_1 g10334 g10334.t12 exon g10334.t12.exon3 8934000 8934407
chr_1 g10334 g10334.t12 cds g10334.t12.CDS3 8934000 8934407
chr_1 g10334 g10334.t12 exon g10334.t12.exon4 8934468 8934696
chr_1 g10334 g10334.t12 cds g10334.t12.CDS4 8934468 8934696
chr_1 g10334 g10334.t12 exon g10334.t12.exon5 8934759 8934836
chr_1 g10334 g10334.t12 cds g10334.t12.CDS5 8934759 8934836
chr_1 g10334 g10334.t12 exon g10334.t12.exon6 8934917 8934967
chr_1 g10334 g10334.t12 cds g10334.t12.CDS6 8934917 8934967
chr_1 g10334 g10334.t12 exon g10334.t12.exon7 8935028 8935088
chr_1 g10334 g10334.t12 cds g10334.t12.CDS7 8935028 8935055
chr_1 g10334 g10334.t12 TSS g10334.t12 8935652 8935652

Sequences

>g10334.t12 Gene=g10334 Length=1302
CTTAAACCAGAATATGCCAAAGCAGCAGAATTGATGAGAACTGATGATCCTCCAATTACT
CTTGTCAAAGTTGATTGTACAGAAGGCGGCAAGGATACTTGCAGCAAATTCGGTGTTTCT
GGATATCCCACTCTCAAAATTTTCAGAAACGGTGAAAATCCTCAGGATTATAATGGTCCA
CGTGAAGCAAGTGGTATTGTGAAATATATGAGAGCACAAGTTGGTCCATCATCAAAGGAT
CTTCTAACAGTTGAAGCATATGAAAAGTTCTTGGGTGTTCAAGAGGGTGCCGTAGTTGGA
TTCTTTGAAAAAGAAACGGATTTGAAGACTGTTTTCTTAAAATATGCCGATTTGCAACGT
GAGAAACTTCGCTTTGCACATTCAAGTGATCCAGAAATTCTCAAGAAAGTTGGCGAAACA
AACGCTATTCTTCTTTATCGTGCACCACAATTGAGTAATAAGTTTGAACCATCTTTTGTT
AAATTCACTGGAAAAGATTCAAGTGATCTTAAAGAATTTGTTAAGAAGAACTTCCACGGT
TTAGTTGGTGTACGTAGTCGTGATACTATTACTGATTTCAACAATCCATTGGTAACTGCA
TATTATGCTGTTGATTATATTAAAAATGCAAAAGGCACAAACTACTGGCGCAATCGTGTA
CTTAAAGTTGCCAAAGAATGGGAAGGTAAAATCAATTTTGCTATTGCTGCTAAAGATGAA
TTCCAACATGAATTGAATGAATATGGTTACGATTATGTCGGTGATAAACCAATAATTTTG
GCTCGTGACGCTCAAAATCAAAAGTTCATCATGAAAGATGAGTTTTCTGTTGACAATCTT
CAAGCATTTGTCAATGATCTTTATGAAGGCAATCTGGAGCCTTACGTTAAATCAGAAGCA
ATTCCAGTCGATCAAGATGGCCCAGTTACAGTTGTAGTTGCAAAGAACTTTAATGAGGCT
GTTCCAAAAGATAAGGATGTTTTAATCGAATTCTACGCACCATGGTGTGGTCATTGCAAA
AAATTAGCTCCAACATTCGATGAATTAGGAACAAAATTGAAGGGTGAAGATGTTGTTATT
GCCAAAATGGATGCTACTGCAAACGATGTTCCTCCTCAATTTGATGTTCGCGGATTCCCG
ACACTCTTCTGGTTGCCTAAGGGCGCTCATGATAAACCAGTTAGATACGATGGCGGTCGT
GAATTGAACGATTTTATCAGCTACATCAGTAAACACGCTACAAATGAATTAAAAGGATAC
GATCGCTCTGGAAACGAAAAGAAACAAAAGACAGAATTGTAA

>g10334.t12 Gene=g10334 Length=422
MRTDDPPITLVKVDCTEGGKDTCSKFGVSGYPTLKIFRNGENPQDYNGPREASGIVKYMR
AQVGPSSKDLLTVEAYEKFLGVQEGAVVGFFEKETDLKTVFLKYADLQREKLRFAHSSDP
EILKKVGETNAILLYRAPQLSNKFEPSFVKFTGKDSSDLKEFVKKNFHGLVGVRSRDTIT
DFNNPLVTAYYAVDYIKNAKGTNYWRNRVLKVAKEWEGKINFAIAAKDEFQHELNEYGYD
YVGDKPIILARDAQNQKFIMKDEFSVDNLQAFVNDLYEGNLEPYVKSEAIPVDQDGPVTV
VVAKNFNEAVPKDKDVLIEFYAPWCGHCKKLAPTFDELGTKLKGEDVVIAKMDATANDVP
PQFDVRGFPTLFWLPKGAHDKPVRYDGGRELNDFISYISKHATNELKGYDRSGNEKKQKT
EL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g10334.t12 CDD cd02961 PDI_a_family 4 59 2.70409E-16
17 g10334.t12 CDD cd03073 PDI_b’_ERp72_ERp57 171 276 1.72303E-38
19 g10334.t12 CDD cd02995 PDI_a_PDI_a’_C 297 398 1.61112E-50
16 g10334.t12 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 63 2.6E-16
13 g10334.t12 Gene3D G3DSA:3.40.30.10 Glutaredoxin 64 173 2.2E-30
15 g10334.t12 Gene3D G3DSA:3.40.30.10 Glutaredoxin 176 279 1.4E-34
14 g10334.t12 Gene3D G3DSA:3.40.30.10 Glutaredoxin 285 421 1.5E-40
4 g10334.t12 PANTHER PTHR18929:SF60 PROTEIN DISULFIDE-ISOMERASE 8 406 4.3E-129
5 g10334.t12 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 8 406 4.3E-129
8 g10334.t12 PRINTS PR00421 Thioredoxin family signature 316 324 5.4E-6
7 g10334.t12 PRINTS PR00421 Thioredoxin family signature 324 333 5.4E-6
6 g10334.t12 PRINTS PR00421 Thioredoxin family signature 364 375 5.4E-6
2 g10334.t12 Pfam PF00085 Thioredoxin 7 60 9.6E-11
1 g10334.t12 Pfam PF13848 Thioredoxin-like domain 92 275 2.6E-32
3 g10334.t12 Pfam PF00085 Thioredoxin 298 399 1.0E-27
20 g10334.t12 ProSitePatterns PS00194 Thioredoxin family active site. 317 335 -
23 g10334.t12 ProSiteProfiles PS51352 Thioredoxin domain profile. 276 403 15.679
12 g10334.t12 SUPERFAMILY SSF52833 Thioredoxin-like 4 64 1.31E-13
11 g10334.t12 SUPERFAMILY SSF52833 Thioredoxin-like 68 167 7.21E-12
10 g10334.t12 SUPERFAMILY SSF52833 Thioredoxin-like 169 295 7.94E-17
9 g10334.t12 SUPERFAMILY SSF52833 Thioredoxin-like 262 402 3.43E-33
21 g10334.t12 TIGRFAM TIGR01130 ER_PDI_fam: protein disulfide isomerase 3 421 3.5E-133
22 g10334.t12 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 301 401 1.5E-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