Gene loci information

Transcript annotation

  • This transcript has been annotated as Thioredoxin.

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 g11995 g11995.t7 TSS g11995.t7 20230944 20230944
chr_1 g11995 g11995.t7 isoform g11995.t7 20230993 20232567
chr_1 g11995 g11995.t7 exon g11995.t7.exon1 20230993 20230995
chr_1 g11995 g11995.t7 cds g11995.t7.CDS1 20230993 20230995
chr_1 g11995 g11995.t7 exon g11995.t7.exon2 20231627 20231773
chr_1 g11995 g11995.t7 cds g11995.t7.CDS2 20231627 20231773
chr_1 g11995 g11995.t7 exon g11995.t7.exon3 20231913 20232567
chr_1 g11995 g11995.t7 cds g11995.t7.CDS3 20231913 20232065
chr_1 g11995 g11995.t7 TTS g11995.t7 20232564 20232564

Sequences

>g11995.t7 Gene=g11995 Length=805
ATGGCTGATTTCGATGCACAACTTGAAAAAGCTGGAGATCTCTTGGTAATCGTAGATTTC
TTCGCAACATGGTGCGGTCCATGTAAGATGATTGCTCCAAAGCTCGAAGAATTTTCAAAC
ACTTACAGCGATAAAATCGTTGTTGTTAAGGTTGACGTTGATGAATGCGAAGACTTGGCT
GTTCAATACAATATTTCGTCCATGCCTACATTTGTTTTCATCAAGAAAGGTCAGCAAATT
GATAGTTTTTCCGGCGCCAATGCAGAAAAACTCGAAAAATATATTACTCAGCACACATCT
TAAGTGAATCAATTACTTTACACAACAATAATATGAGAACATTTCTCGTGCAGCAGTATT
TTCAACAAGATCGAAACATCAATAATTTTATGGCCTTTTCAAAAACATACACACACTTAA
TTGAGACATATATTTAATATACATTTGAATGCTTTATTAAAAGTTTTTCTCATAGAAAAT
GAAACAAACAATCTAAGCAGTTATATGAAATTGAATTTTAGACTTGATTTGTTACACGAG
AGGTTTTTTGTAATCTATGTTAATGTTAAAACCATTTTGTTTTAATTTAAAGTCTTTTTC
TCTTTTAAGATCTTTTTCTATGAAATTTTTTGAACTTATTAAAATACAAATTTTGATTAA
GTAATTCCATACACAAAATGTTACTTTTATTCTTTTGAACATTTAATTCAATATGAAAAA
ACAGGTTTTTAGCAAATATTTTGTTAATCGATATAACACCATTTATTGAGTAATAAAATA
TTTATTCTGAAAAGAGAATGAGAAA

>g11995.t7 Gene=g11995 Length=100
MADFDAQLEKAGDLLVIVDFFATWCGPCKMIAPKLEEFSNTYSDKIVVVKVDVDECEDLA
VQYNISSMPTFVFIKKGQQIDSFSGANAEKLEKYITQHTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11995.t7 CDD cd02947 TRX_family 2 95 2.705E-28
7 g11995.t7 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 100 1.1E-35
2 g11995.t7 PANTHER PTHR46115 THIOREDOXIN-LIKE PROTEIN 1 2 100 1.4E-44
8 g11995.t7 PIRSF PIRSF000077 Thioredoxin 1 99 3.0E-34
4 g11995.t7 PRINTS PR00421 Thioredoxin family signature 16 24 3.5E-8
3 g11995.t7 PRINTS PR00421 Thioredoxin family signature 24 33 3.5E-8
5 g11995.t7 PRINTS PR00421 Thioredoxin family signature 64 75 3.5E-8
1 g11995.t7 Pfam PF00085 Thioredoxin 2 96 4.2E-33
10 g11995.t7 ProSitePatterns PS00194 Thioredoxin family active site. 17 35 -
12 g11995.t7 ProSiteProfiles PS51352 Thioredoxin domain profile. 1 100 13.806
6 g11995.t7 SUPERFAMILY SSF52833 Thioredoxin-like 2 98 2.43E-35
11 g11995.t7 TIGRFAM TIGR01068 thioredoxin: thioredoxin 10 98 4.9E-33

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:0015035 protein-disulfide reductase activity MF
GO:0006662 glycerol ether metabolic process BP
GO:0045454 cell redox homeostasis BP

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