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.t24 TTS g10334.t24 8933125 8933125
chr_1 g10334 g10334.t24 isoform g10334.t24 8933413 8935590
chr_1 g10334 g10334.t24 exon g10334.t24.exon1 8933413 8933710
chr_1 g10334 g10334.t24 cds g10334.t24.CDS1 8933413 8933710
chr_1 g10334 g10334.t24 exon g10334.t24.exon2 8933766 8933942
chr_1 g10334 g10334.t24 cds g10334.t24.CDS2 8933766 8933942
chr_1 g10334 g10334.t24 exon g10334.t24.exon3 8934000 8934407
chr_1 g10334 g10334.t24 cds g10334.t24.CDS3 8934000 8934407
chr_1 g10334 g10334.t24 exon g10334.t24.exon4 8934468 8934696
chr_1 g10334 g10334.t24 cds g10334.t24.CDS4 8934468 8934696
chr_1 g10334 g10334.t24 exon g10334.t24.exon5 8934759 8934836
chr_1 g10334 g10334.t24 cds g10334.t24.CDS5 8934759 8934836
chr_1 g10334 g10334.t24 exon g10334.t24.exon6 8934917 8934967
chr_1 g10334 g10334.t24 cds g10334.t24.CDS6 8934917 8934967
chr_1 g10334 g10334.t24 exon g10334.t24.exon7 8935028 8935088
chr_1 g10334 g10334.t24 cds g10334.t24.CDS7 8935028 8935088
chr_1 g10334 g10334.t24 exon g10334.t24.exon8 8935459 8935590
chr_1 g10334 g10334.t24 cds g10334.t24.CDS8 8935459 8935590
chr_1 g10334 g10334.t24 TSS g10334.t24 8935652 8935652

Sequences

>g10334.t24 Gene=g10334 Length=1434
ATGAAATTACTTGTTTTTCTGTCATTTTTGTTTGTTGCTGAGTTGGCTCTCTCGGCTGAG
AGTGATGTTCTTGAATTGACTGATTCTGATTTTGAAACTACAATCAAAGAATATCCAACA
GTGTTGGCAATGCTTAAACCAGAATATGCCAAAGCAGCAGAATTGATGAGAACTGATGAT
CCTCCAATTACTCTTGTCAAAGTTGATTGTACAGAAGGCGGCAAGGATACTTGCAGCAAA
TTCGGTGTTTCTGGATATCCCACTCTCAAAATTTTCAGAAACGGTGAAAATCCTCAGGAT
TATAATGGTCCACGTGAAGCAAGTGGTATTGTGAAATATATGAGAGCACAAGTTGGTCCA
TCATCAAAGGATCTTCTAACAGTTGAAGCATATGAAAAGTTCTTGGGTGTTCAAGAGGGT
GCCGTAGTTGGATTCTTTGAAAAAGAAACGGATTTGAAGACTGTTTTCTTAAAATATGCC
GATTTGCAACGTGAGAAACTTCGCTTTGCACATTCAAGTGATCCAGAAATTCTCAAGAAA
GTTGGCGAAACAAACGCTATTCTTCTTTATCGTGCACCACAATTGAGTAATAAGTTTGAA
CCATCTTTTGTTAAATTCACTGGAAAAGATTCAAGTGATCTTAAAGAATTTGTTAAGAAG
AACTTCCACGGTTTAGTTGGTGTACGTAGTCGTGATACTATTACTGATTTCAACAATCCA
TTGGTAACTGCATATTATGCTGTTGATTATATTAAAAATGCAAAAGGCACAAACTACTGG
CGCAATCGTGTACTTAAAGTTGCCAAAGAATGGGAAGGTAAAATCAATTTTGCTATTGCT
GCTAAAGATGAATTCCAACATGAATTGAATGAATATGGTTACGATTATGTCGGTGATAAA
CCAATAATTTTGGCTCGTGACGCTCAAAATCAAAAGTTCATCATGAAAGATGAGTTTTCT
GTTGACAATCTTCAAGCATTTGTCAATGATCTTTATGAAGGCAATCTGGAGCCTTACGTT
AAATCAGAAGCAATTCCAGTCGATCAAGATGGCCCAGTTACAGTTGTAGTTGCAAAGAAC
TTTAATGAGGCTGTTCCAAAAGATAAGGATGTTTTAATCGAATTCTACGCACCATGGTGT
GGTCATTGCAAAAAATTAGCTCCAACATTCGATGAATTAGGAACAAAATTGAAGGGTGAA
GATGTTGTTATTGCCAAAATGGATGCTACTGCAAACGATGTTCCTCCTCAATTTGATGTT
CGCGGATTCCCGACACTCTTCTGGTTGCCTAAGGGCGCTCATGATAAACCAGTTAGATAC
GATGGCGGTCGTGAATTGAACGATTTTATCAGCTACATCAGTAAACACGCTACAAATGAA
TTAAAAGGATACGATCGCTCTGGAAACGAAAAGAAACAAAAGACAGAATTGTAA

>g10334.t24 Gene=g10334 Length=477
MKLLVFLSFLFVAELALSAESDVLELTDSDFETTIKEYPTVLAMLKPEYAKAAELMRTDD
PPITLVKVDCTEGGKDTCSKFGVSGYPTLKIFRNGENPQDYNGPREASGIVKYMRAQVGP
SSKDLLTVEAYEKFLGVQEGAVVGFFEKETDLKTVFLKYADLQREKLRFAHSSDPEILKK
VGETNAILLYRAPQLSNKFEPSFVKFTGKDSSDLKEFVKKNFHGLVGVRSRDTITDFNNP
LVTAYYAVDYIKNAKGTNYWRNRVLKVAKEWEGKINFAIAAKDEFQHELNEYGYDYVGDK
PIILARDAQNQKFIMKDEFSVDNLQAFVNDLYEGNLEPYVKSEAIPVDQDGPVTVVVAKN
FNEAVPKDKDVLIEFYAPWCGHCKKLAPTFDELGTKLKGEDVVIAKMDATANDVPPQFDV
RGFPTLFWLPKGAHDKPVRYDGGRELNDFISYISKHATNELKGYDRSGNEKKQKTEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g10334.t24 CDD cd02961 PDI_a_family 24 114 2.3464E-24
24 g10334.t24 CDD cd03073 PDI_b’_ERp72_ERp57 226 331 4.11685E-38
26 g10334.t24 CDD cd02995 PDI_a_PDI_a’_C 352 453 4.79736E-50
15 g10334.t24 Gene3D G3DSA:3.40.30.10 Glutaredoxin 14 118 1.9E-21
18 g10334.t24 Gene3D G3DSA:3.40.30.10 Glutaredoxin 119 228 2.8E-30
16 g10334.t24 Gene3D G3DSA:3.40.30.10 Glutaredoxin 231 334 1.8E-34
17 g10334.t24 Gene3D G3DSA:3.40.30.10 Glutaredoxin 340 476 1.9E-40
4 g10334.t24 PANTHER PTHR18929:SF60 PROTEIN DISULFIDE-ISOMERASE 17 461 2.9E-132
5 g10334.t24 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 17 461 2.9E-132
6 g10334.t24 PRINTS PR00421 Thioredoxin family signature 371 379 7.5E-6
7 g10334.t24 PRINTS PR00421 Thioredoxin family signature 379 388 7.5E-6
8 g10334.t24 PRINTS PR00421 Thioredoxin family signature 419 430 7.5E-6
3 g10334.t24 Pfam PF00085 Thioredoxin 44 115 1.7E-13
1 g10334.t24 Pfam PF13848 Thioredoxin-like domain 147 330 3.4E-32
2 g10334.t24 Pfam PF00085 Thioredoxin 353 454 1.3E-27
20 g10334.t24 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
21 g10334.t24 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
22 g10334.t24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 13 -
23 g10334.t24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
19 g10334.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 477 -
28 g10334.t24 ProSitePatterns PS00194 Thioredoxin family active site. 372 390 -
31 g10334.t24 ProSiteProfiles PS51352 Thioredoxin domain profile. 331 458 15.679
11 g10334.t24 SUPERFAMILY SSF52833 Thioredoxin-like 17 119 1.45E-21
9 g10334.t24 SUPERFAMILY SSF52833 Thioredoxin-like 123 222 9.79E-12
12 g10334.t24 SUPERFAMILY SSF52833 Thioredoxin-like 223 350 1.1E-16
10 g10334.t24 SUPERFAMILY SSF52833 Thioredoxin-like 317 457 4.5E-33
14 g10334.t24 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -
27 g10334.t24 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 18 -
13 g10334.t24 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 18 -
29 g10334.t24 TIGRFAM TIGR01130 ER_PDI_fam: protein disulfide isomerase 21 476 3.9E-141
30 g10334.t24 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 356 456 1.9E-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