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.t11 TTS g10334.t11 8933125 8933125
chr_1 g10334 g10334.t11 isoform g10334.t11 8933413 8935027
chr_1 g10334 g10334.t11 exon g10334.t11.exon1 8933413 8933710
chr_1 g10334 g10334.t11 cds g10334.t11.CDS1 8933413 8933710
chr_1 g10334 g10334.t11 exon g10334.t11.exon2 8933766 8933942
chr_1 g10334 g10334.t11 cds g10334.t11.CDS2 8933766 8933942
chr_1 g10334 g10334.t11 exon g10334.t11.exon3 8934000 8934407
chr_1 g10334 g10334.t11 cds g10334.t11.CDS3 8934000 8934407
chr_1 g10334 g10334.t11 exon g10334.t11.exon4 8934468 8934696
chr_1 g10334 g10334.t11 cds g10334.t11.CDS4 8934468 8934696
chr_1 g10334 g10334.t11 exon g10334.t11.exon5 8934759 8934836
chr_1 g10334 g10334.t11 cds g10334.t11.CDS5 8934759 8934836
chr_1 g10334 g10334.t11 exon g10334.t11.exon6 8934917 8935027
chr_1 g10334 g10334.t11 cds g10334.t11.CDS6 8934917 8935025
chr_1 g10334 g10334.t11 TSS g10334.t11 8935652 8935652

Sequences

>g10334.t11 Gene=g10334 Length=1301
GTATGTTTTGCAAACTCATATTTAAATTTATCTTATTCTGTAATAAATTTCTTTTATTAG
TTGTCAAAGTTGATTGTACAGAAGGCGGCAAGGATACTTGCAGCAAATTCGGTGTTTCTG
GATATCCCACTCTCAAAATTTTCAGAAACGGTGAAAATCCTCAGGATTATAATGGTCCAC
GTGAAGCAAGTGGTATTGTGAAATATATGAGAGCACAAGTTGGTCCATCATCAAAGGATC
TTCTAACAGTTGAAGCATATGAAAAGTTCTTGGGTGTTCAAGAGGGTGCCGTAGTTGGAT
TCTTTGAAAAAGAAACGGATTTGAAGACTGTTTTCTTAAAATATGCCGATTTGCAACGTG
AGAAACTTCGCTTTGCACATTCAAGTGATCCAGAAATTCTCAAGAAAGTTGGCGAAACAA
ACGCTATTCTTCTTTATCGTGCACCACAATTGAGTAATAAGTTTGAACCATCTTTTGTTA
AATTCACTGGAAAAGATTCAAGTGATCTTAAAGAATTTGTTAAGAAGAACTTCCACGGTT
TAGTTGGTGTACGTAGTCGTGATACTATTACTGATTTCAACAATCCATTGGTAACTGCAT
ATTATGCTGTTGATTATATTAAAAATGCAAAAGGCACAAACTACTGGCGCAATCGTGTAC
TTAAAGTTGCCAAAGAATGGGAAGGTAAAATCAATTTTGCTATTGCTGCTAAAGATGAAT
TCCAACATGAATTGAATGAATATGGTTACGATTATGTCGGTGATAAACCAATAATTTTGG
CTCGTGACGCTCAAAATCAAAAGTTCATCATGAAAGATGAGTTTTCTGTTGACAATCTTC
AAGCATTTGTCAATGATCTTTATGAAGGCAATCTGGAGCCTTACGTTAAATCAGAAGCAA
TTCCAGTCGATCAAGATGGCCCAGTTACAGTTGTAGTTGCAAAGAACTTTAATGAGGCTG
TTCCAAAAGATAAGGATGTTTTAATCGAATTCTACGCACCATGGTGTGGTCATTGCAAAA
AATTAGCTCCAACATTCGATGAATTAGGAACAAAATTGAAGGGTGAAGATGTTGTTATTG
CCAAAATGGATGCTACTGCAAACGATGTTCCTCCTCAATTTGATGTTCGCGGATTCCCGA
CACTCTTCTGGTTGCCTAAGGGCGCTCATGATAAACCAGTTAGATACGATGGCGGTCGTG
AATTGAACGATTTTATCAGCTACATCAGTAAACACGCTACAAATGAATTAAAAGGATACG
ATCGCTCTGGAAACGAAAAGAAACAAAAGACAGAATTGTAA

>g10334.t11 Gene=g10334 Length=432
MFCKLIFKFILFCNKFLLLVVKVDCTEGGKDTCSKFGVSGYPTLKIFRNGENPQDYNGPR
EASGIVKYMRAQVGPSSKDLLTVEAYEKFLGVQEGAVVGFFEKETDLKTVFLKYADLQRE
KLRFAHSSDPEILKKVGETNAILLYRAPQLSNKFEPSFVKFTGKDSSDLKEFVKKNFHGL
VGVRSRDTITDFNNPLVTAYYAVDYIKNAKGTNYWRNRVLKVAKEWEGKINFAIAAKDEF
QHELNEYGYDYVGDKPIILARDAQNQKFIMKDEFSVDNLQAFVNDLYEGNLEPYVKSEAI
PVDQDGPVTVVVAKNFNEAVPKDKDVLIEFYAPWCGHCKKLAPTFDELGTKLKGEDVVIA
KMDATANDVPPQFDVRGFPTLFWLPKGAHDKPVRYDGGRELNDFISYISKHATNELKGYD
RSGNEKKQKTEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
24 g10334.t11 CDD cd03073 PDI_b’_ERp72_ERp57 181 286 3.0273E-38
25 g10334.t11 CDD cd02995 PDI_a_PDI_a’_C 307 408 5.32142E-50
18 g10334.t11 Gene3D G3DSA:3.40.30.10 Glutaredoxin 14 73 6.2E-15
15 g10334.t11 Gene3D G3DSA:3.40.30.10 Glutaredoxin 74 183 2.3E-30
16 g10334.t11 Gene3D G3DSA:3.40.30.10 Glutaredoxin 186 289 1.5E-34
17 g10334.t11 Gene3D G3DSA:3.40.30.10 Glutaredoxin 295 431 1.6E-40
4 g10334.t11 PANTHER PTHR18929:SF60 PROTEIN DISULFIDE-ISOMERASE 18 416 2.0E-128
5 g10334.t11 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 18 416 2.0E-128
7 g10334.t11 PRINTS PR00421 Thioredoxin family signature 326 334 5.8E-6
6 g10334.t11 PRINTS PR00421 Thioredoxin family signature 334 343 5.8E-6
8 g10334.t11 PRINTS PR00421 Thioredoxin family signature 374 385 5.8E-6
3 g10334.t11 Pfam PF00085 Thioredoxin 18 70 4.7E-10
1 g10334.t11 Pfam PF13848 Thioredoxin-like domain 102 285 2.7E-32
2 g10334.t11 Pfam PF00085 Thioredoxin 308 409 1.1E-27
20 g10334.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
21 g10334.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 8 -
22 g10334.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 9 20 -
23 g10334.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 21 25 -
19 g10334.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 432 -
26 g10334.t11 ProSitePatterns PS00194 Thioredoxin family active site. 327 345 -
29 g10334.t11 ProSiteProfiles PS51352 Thioredoxin domain profile. 286 413 15.679
12 g10334.t11 SUPERFAMILY SSF52833 Thioredoxin-like 17 74 5.47E-13
9 g10334.t11 SUPERFAMILY SSF52833 Thioredoxin-like 78 177 7.46E-12
11 g10334.t11 SUPERFAMILY SSF52833 Thioredoxin-like 178 305 7.94E-17
10 g10334.t11 SUPERFAMILY SSF52833 Thioredoxin-like 272 412 3.65E-33
14 g10334.t11 SignalP_EUK SignalP-noTM SignalP-noTM 1 25 -
13 g10334.t11 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 23 -
27 g10334.t11 TIGRFAM TIGR01130 ER_PDI_fam: protein disulfide isomerase 20 431 1.7E-130
28 g10334.t11 TIGRFAM TIGR01126 pdi_dom: protein disulfide-isomerase domain 311 411 1.6E-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