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.t1 TTS g10334.t1 8933125 8933125
chr_1 g10334 g10334.t1 isoform g10334.t1 8933413 8935590
chr_1 g10334 g10334.t1 exon g10334.t1.exon1 8933413 8933710
chr_1 g10334 g10334.t1 cds g10334.t1.CDS1 8933413 8933710
chr_1 g10334 g10334.t1 exon g10334.t1.exon2 8933766 8933942
chr_1 g10334 g10334.t1 cds g10334.t1.CDS2 8933766 8933942
chr_1 g10334 g10334.t1 exon g10334.t1.exon3 8934000 8934407
chr_1 g10334 g10334.t1 cds g10334.t1.CDS3 8934000 8934407
chr_1 g10334 g10334.t1 exon g10334.t1.exon4 8934468 8934696
chr_1 g10334 g10334.t1 cds g10334.t1.CDS4 8934468 8934696
chr_1 g10334 g10334.t1 exon g10334.t1.exon5 8934759 8934836
chr_1 g10334 g10334.t1 cds g10334.t1.CDS5 8934759 8934836
chr_1 g10334 g10334.t1 exon g10334.t1.exon6 8934917 8934967
chr_1 g10334 g10334.t1 cds g10334.t1.CDS6 8934917 8934967
chr_1 g10334 g10334.t1 exon g10334.t1.exon7 8935028 8935088
chr_1 g10334 g10334.t1 cds g10334.t1.CDS7 8935028 8935088
chr_1 g10334 g10334.t1 exon g10334.t1.exon8 8935154 8935167
chr_1 g10334 g10334.t1 cds g10334.t1.CDS8 8935154 8935167
chr_1 g10334 g10334.t1 exon g10334.t1.exon9 8935322 8935340
chr_1 g10334 g10334.t1 cds g10334.t1.CDS9 8935322 8935340
chr_1 g10334 g10334.t1 exon g10334.t1.exon10 8935459 8935590
chr_1 g10334 g10334.t1 cds g10334.t1.CDS10 8935459 8935590
chr_1 g10334 g10334.t1 TSS g10334.t1 8935652 8935652

Sequences

>g10334.t1 Gene=g10334 Length=1467
ATGAAATTACTTGTTTTTCTGTCATTTTTGTTTGTTGCTGAGTTGGCTCTCTCGGCTGAG
AGTGATGTTCTTGAATTGACTGATTCTGATTTTGAAACTACAATCAAAGAATATCCAACA
GTGTTGGCAATGTTCTACGCTCCCTGGTGTGGTCATTGCAAAAAACTTAAACCAGAATAT
GCCAAAGCAGCAGAATTGATGAGAACTGATGATCCTCCAATTACTCTTGTCAAAGTTGAT
TGTACAGAAGGCGGCAAGGATACTTGCAGCAAATTCGGTGTTTCTGGATATCCCACTCTC
AAAATTTTCAGAAACGGTGAAAATCCTCAGGATTATAATGGTCCACGTGAAGCAAGTGGT
ATTGTGAAATATATGAGAGCACAAGTTGGTCCATCATCAAAGGATCTTCTAACAGTTGAA
GCATATGAAAAGTTCTTGGGTGTTCAAGAGGGTGCCGTAGTTGGATTCTTTGAAAAAGAA
ACGGATTTGAAGACTGTTTTCTTAAAATATGCCGATTTGCAACGTGAGAAACTTCGCTTT
GCACATTCAAGTGATCCAGAAATTCTCAAGAAAGTTGGCGAAACAAACGCTATTCTTCTT
TATCGTGCACCACAATTGAGTAATAAGTTTGAACCATCTTTTGTTAAATTCACTGGAAAA
GATTCAAGTGATCTTAAAGAATTTGTTAAGAAGAACTTCCACGGTTTAGTTGGTGTACGT
AGTCGTGATACTATTACTGATTTCAACAATCCATTGGTAACTGCATATTATGCTGTTGAT
TATATTAAAAATGCAAAAGGCACAAACTACTGGCGCAATCGTGTACTTAAAGTTGCCAAA
GAATGGGAAGGTAAAATCAATTTTGCTATTGCTGCTAAAGATGAATTCCAACATGAATTG
AATGAATATGGTTACGATTATGTCGGTGATAAACCAATAATTTTGGCTCGTGACGCTCAA
AATCAAAAGTTCATCATGAAAGATGAGTTTTCTGTTGACAATCTTCAAGCATTTGTCAAT
GATCTTTATGAAGGCAATCTGGAGCCTTACGTTAAATCAGAAGCAATTCCAGTCGATCAA
GATGGCCCAGTTACAGTTGTAGTTGCAAAGAACTTTAATGAGGCTGTTCCAAAAGATAAG
GATGTTTTAATCGAATTCTACGCACCATGGTGTGGTCATTGCAAAAAATTAGCTCCAACA
TTCGATGAATTAGGAACAAAATTGAAGGGTGAAGATGTTGTTATTGCCAAAATGGATGCT
ACTGCAAACGATGTTCCTCCTCAATTTGATGTTCGCGGATTCCCGACACTCTTCTGGTTG
CCTAAGGGCGCTCATGATAAACCAGTTAGATACGATGGCGGTCGTGAATTGAACGATTTT
ATCAGCTACATCAGTAAACACGCTACAAATGAATTAAAAGGATACGATCGCTCTGGAAAC
GAAAAGAAACAAAAGACAGAATTGTAA

>g10334.t1 Gene=g10334 Length=488
MKLLVFLSFLFVAELALSAESDVLELTDSDFETTIKEYPTVLAMFYAPWCGHCKKLKPEY
AKAAELMRTDDPPITLVKVDCTEGGKDTCSKFGVSGYPTLKIFRNGENPQDYNGPREASG
IVKYMRAQVGPSSKDLLTVEAYEKFLGVQEGAVVGFFEKETDLKTVFLKYADLQREKLRF
AHSSDPEILKKVGETNAILLYRAPQLSNKFEPSFVKFTGKDSSDLKEFVKKNFHGLVGVR
SRDTITDFNNPLVTAYYAVDYIKNAKGTNYWRNRVLKVAKEWEGKINFAIAAKDEFQHEL
NEYGYDYVGDKPIILARDAQNQKFIMKDEFSVDNLQAFVNDLYEGNLEPYVKSEAIPVDQ
DGPVTVVVAKNFNEAVPKDKDVLIEFYAPWCGHCKKLAPTFDELGTKLKGEDVVIAKMDA
TANDVPPQFDVRGFPTLFWLPKGAHDKPVRYDGGRELNDFISYISKHATNELKGYDRSGN
EKKQKTEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
25 g10334.t1 CDD cd02961 PDI_a_family 24 125 6.60432E-40
24 g10334.t1 CDD cd03073 PDI_b’_ERp72_ERp57 237 342 2.23858E-38
26 g10334.t1 CDD cd02995 PDI_a_PDI_a’_C 363 464 5.35753E-50
16 g10334.t1 Gene3D G3DSA:3.40.30.10 Glutaredoxin 15 128 2.9E-37
17 g10334.t1 Gene3D G3DSA:3.40.30.10 Glutaredoxin 129 239 2.9E-30
15 g10334.t1 Gene3D G3DSA:3.40.30.10 Glutaredoxin 242 345 1.8E-34
18 g10334.t1 Gene3D G3DSA:3.40.30.10 Glutaredoxin 351 487 2.0E-40
4 g10334.t1 PANTHER PTHR18929:SF60 PROTEIN DISULFIDE-ISOMERASE 17 472 1.6E-147
5 g10334.t1 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 17 472 1.6E-147
7 g10334.t1 PRINTS PR00421 Thioredoxin family signature 41 49 9.2E-7
8 g10334.t1 PRINTS PR00421 Thioredoxin family signature 49 58 9.2E-7
6 g10334.t1 PRINTS PR00421 Thioredoxin family signature 93 104 9.2E-7
3 g10334.t1 Pfam PF00085 Thioredoxin 23 126 1.6E-28
1 g10334.t1 Pfam PF13848 Thioredoxin-like domain 158 341 3.6E-32
2 g10334.t1 Pfam PF00085 Thioredoxin 364 465 1.3E-27
20 g10334.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
21 g10334.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
22 g10334.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 13 -
23 g10334.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
19 g10334.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 488 -
29 g10334.t1 ProSitePatterns PS00194 Thioredoxin family active site. 42 60 -
28 g10334.t1 ProSitePatterns PS00194 Thioredoxin family active site. 383 401 -
33 g10334.t1 ProSiteProfiles PS51352 Thioredoxin domain profile. 15 130 13.184
34 g10334.t1 ProSiteProfiles PS51352 Thioredoxin domain profile. 342 469 15.679
12 g10334.t1 SUPERFAMILY SSF52833 Thioredoxin-like 17 130 5.21E-35
11 g10334.t1 SUPERFAMILY SSF52833 Thioredoxin-like 134 233 1.03E-11
10 g10334.t1 SUPERFAMILY SSF52833 Thioredoxin-like 234 361 1.17E-16
9 g10334.t1 SUPERFAMILY SSF52833 Thioredoxin-like 328 468 4.5E-33
14 g10334.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -
27 g10334.t1 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 18 -
13 g10334.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 18 -
30 g10334.t1 TIGRFAM TIGR01130 ER_PDI_fam: protein disulfide isomerase 21 487 8.2E-161
31 g10334.t1 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 26 128 8.9E-33
32 g10334.t1 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 367 467 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

Pathway

  • This transcript belongs to the following pathways

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