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.t16 TTS g10334.t16 8933125 8933125
chr_1 g10334 g10334.t16 isoform g10334.t16 8933413 8935590
chr_1 g10334 g10334.t16 exon g10334.t16.exon1 8933413 8933710
chr_1 g10334 g10334.t16 cds g10334.t16.CDS1 8933413 8933710
chr_1 g10334 g10334.t16 exon g10334.t16.exon2 8933766 8933942
chr_1 g10334 g10334.t16 cds g10334.t16.CDS2 8933766 8933942
chr_1 g10334 g10334.t16 exon g10334.t16.exon3 8934000 8934407
chr_1 g10334 g10334.t16 cds g10334.t16.CDS3 8934000 8934407
chr_1 g10334 g10334.t16 exon g10334.t16.exon4 8934468 8934696
chr_1 g10334 g10334.t16 cds g10334.t16.CDS4 8934468 8934696
chr_1 g10334 g10334.t16 exon g10334.t16.exon5 8934759 8934836
chr_1 g10334 g10334.t16 cds g10334.t16.CDS5 8934759 8934836
chr_1 g10334 g10334.t16 exon g10334.t16.exon6 8934917 8934967
chr_1 g10334 g10334.t16 cds g10334.t16.CDS6 8934917 8934967
chr_1 g10334 g10334.t16 exon g10334.t16.exon7 8935028 8935088
chr_1 g10334 g10334.t16 cds g10334.t16.CDS7 8935028 8935055
chr_1 g10334 g10334.t16 exon g10334.t16.exon8 8935448 8935590
chr_1 g10334 g10334.t16 TSS g10334.t16 8935652 8935652

Sequences

>g10334.t16 Gene=g10334 Length=1445
ATGAAATTACTTGTTTTTCTGTCATTTTTGTTTGTTGCTGAGTTGGCTCTCTCGGCTGAG
AGTGATGTTCTTGAATTGACTGATTCTGATTTTGAAACTACAATCAAAGAATATCCAACA
GTGTTGGCAATGGTAATATAAAACTTAAACCAGAATATGCCAAAGCAGCAGAATTGATGA
GAACTGATGATCCTCCAATTACTCTTGTCAAAGTTGATTGTACAGAAGGCGGCAAGGATA
CTTGCAGCAAATTCGGTGTTTCTGGATATCCCACTCTCAAAATTTTCAGAAACGGTGAAA
ATCCTCAGGATTATAATGGTCCACGTGAAGCAAGTGGTATTGTGAAATATATGAGAGCAC
AAGTTGGTCCATCATCAAAGGATCTTCTAACAGTTGAAGCATATGAAAAGTTCTTGGGTG
TTCAAGAGGGTGCCGTAGTTGGATTCTTTGAAAAAGAAACGGATTTGAAGACTGTTTTCT
TAAAATATGCCGATTTGCAACGTGAGAAACTTCGCTTTGCACATTCAAGTGATCCAGAAA
TTCTCAAGAAAGTTGGCGAAACAAACGCTATTCTTCTTTATCGTGCACCACAATTGAGTA
ATAAGTTTGAACCATCTTTTGTTAAATTCACTGGAAAAGATTCAAGTGATCTTAAAGAAT
TTGTTAAGAAGAACTTCCACGGTTTAGTTGGTGTACGTAGTCGTGATACTATTACTGATT
TCAACAATCCATTGGTAACTGCATATTATGCTGTTGATTATATTAAAAATGCAAAAGGCA
CAAACTACTGGCGCAATCGTGTACTTAAAGTTGCCAAAGAATGGGAAGGTAAAATCAATT
TTGCTATTGCTGCTAAAGATGAATTCCAACATGAATTGAATGAATATGGTTACGATTATG
TCGGTGATAAACCAATAATTTTGGCTCGTGACGCTCAAAATCAAAAGTTCATCATGAAAG
ATGAGTTTTCTGTTGACAATCTTCAAGCATTTGTCAATGATCTTTATGAAGGCAATCTGG
AGCCTTACGTTAAATCAGAAGCAATTCCAGTCGATCAAGATGGCCCAGTTACAGTTGTAG
TTGCAAAGAACTTTAATGAGGCTGTTCCAAAAGATAAGGATGTTTTAATCGAATTCTACG
CACCATGGTGTGGTCATTGCAAAAAATTAGCTCCAACATTCGATGAATTAGGAACAAAAT
TGAAGGGTGAAGATGTTGTTATTGCCAAAATGGATGCTACTGCAAACGATGTTCCTCCTC
AATTTGATGTTCGCGGATTCCCGACACTCTTCTGGTTGCCTAAGGGCGCTCATGATAAAC
CAGTTAGATACGATGGCGGTCGTGAATTGAACGATTTTATCAGCTACATCAGTAAACACG
CTACAAATGAATTAAAAGGATACGATCGCTCTGGAAACGAAAAGAAACAAAAGACAGAAT
TGTAA

>g10334.t16 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.t16 CDD cd02961 PDI_a_family 4 59 2.70409E-16
17 g10334.t16 CDD cd03073 PDI_b’_ERp72_ERp57 171 276 1.72303E-38
19 g10334.t16 CDD cd02995 PDI_a_PDI_a’_C 297 398 1.61112E-50
16 g10334.t16 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 63 2.6E-16
13 g10334.t16 Gene3D G3DSA:3.40.30.10 Glutaredoxin 64 173 2.2E-30
15 g10334.t16 Gene3D G3DSA:3.40.30.10 Glutaredoxin 176 279 1.4E-34
14 g10334.t16 Gene3D G3DSA:3.40.30.10 Glutaredoxin 285 421 1.5E-40
4 g10334.t16 PANTHER PTHR18929:SF60 PROTEIN DISULFIDE-ISOMERASE 8 406 4.3E-129
5 g10334.t16 PANTHER PTHR18929 PROTEIN DISULFIDE ISOMERASE 8 406 4.3E-129
8 g10334.t16 PRINTS PR00421 Thioredoxin family signature 316 324 5.4E-6
7 g10334.t16 PRINTS PR00421 Thioredoxin family signature 324 333 5.4E-6
6 g10334.t16 PRINTS PR00421 Thioredoxin family signature 364 375 5.4E-6
2 g10334.t16 Pfam PF00085 Thioredoxin 7 60 9.6E-11
1 g10334.t16 Pfam PF13848 Thioredoxin-like domain 92 275 2.6E-32
3 g10334.t16 Pfam PF00085 Thioredoxin 298 399 1.0E-27
20 g10334.t16 ProSitePatterns PS00194 Thioredoxin family active site. 317 335 -
23 g10334.t16 ProSiteProfiles PS51352 Thioredoxin domain profile. 276 403 15.679
12 g10334.t16 SUPERFAMILY SSF52833 Thioredoxin-like 4 64 1.31E-13
11 g10334.t16 SUPERFAMILY SSF52833 Thioredoxin-like 68 167 7.21E-12
10 g10334.t16 SUPERFAMILY SSF52833 Thioredoxin-like 169 295 7.94E-17
9 g10334.t16 SUPERFAMILY SSF52833 Thioredoxin-like 262 402 3.43E-33
21 g10334.t16 TIGRFAM TIGR01130 ER_PDI_fam: protein disulfide isomerase 3 421 3.5E-133
22 g10334.t16 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