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.t8 TSS g11995.t8 20230944 20230944
chr_1 g11995 g11995.t8 isoform g11995.t8 20230993 20232567
chr_1 g11995 g11995.t8 exon g11995.t8.exon1 20230993 20231344
chr_1 g11995 g11995.t8 cds g11995.t8.CDS1 20231270 20231344
chr_1 g11995 g11995.t8 exon g11995.t8.exon2 20231627 20231773
chr_1 g11995 g11995.t8 cds g11995.t8.CDS2 20231627 20231773
chr_1 g11995 g11995.t8 exon g11995.t8.exon3 20231913 20232567
chr_1 g11995 g11995.t8 cds g11995.t8.CDS3 20231913 20232065
chr_1 g11995 g11995.t8 TTS g11995.t8 20232564 20232564

Sequences

>g11995.t8 Gene=g11995 Length=1154
ATGGTGTACCTTATTAAGGATAAAGTAAGTATATAAAAATGTAAATAAAAAAATAAAGTG
CAAATATCAATAAAATATGAAATAAAAATTCATACATGAAATATTAGGATAATTTCCTCA
TTAAAACAAATGAAAAATCATTAAAGTGCTGTAATATGATAAGAGAAATTGCTTGTTACC
ATGTTCAATTTTGTATTATAATCGCAGAAATCTATTTCGCAATTTTACGCGAAGATTTTT
CATATTTTCTGTTTTCAAAATTAATCGTGACGAGAAAATGTCTGCGGCTGATAAATTCTG
TTCATGTGTTTGTTTCAAGAGGCAAGAAATCAATCATTTTAACGGGTGCAAAGCTGATTT
CGATGCACAACTTGAAAAAGCTGGAGATCTCTTGGTAATCGTAGATTTCTTCGCAACATG
GTGCGGTCCATGTAAGATGATTGCTCCAAAGCTCGAAGAATTTTCAAACACTTACAGCGA
TAAAATCGTTGTTGTTAAGGTTGACGTTGATGAATGCGAAGACTTGGCTGTTCAATACAA
TATTTCGTCCATGCCTACATTTGTTTTCATCAAGAAAGGTCAGCAAATTGATAGTTTTTC
CGGCGCCAATGCAGAAAAACTCGAAAAATATATTACTCAGCACACATCTTAAGTGAATCA
ATTACTTTACACAACAATAATATGAGAACATTTCTCGTGCAGCAGTATTTTCAACAAGAT
CGAAACATCAATAATTTTATGGCCTTTTCAAAAACATACACACACTTAATTGAGACATAT
ATTTAATATACATTTGAATGCTTTATTAAAAGTTTTTCTCATAGAAAATGAAACAAACAA
TCTAAGCAGTTATATGAAATTGAATTTTAGACTTGATTTGTTACACGAGAGGTTTTTTGT
AATCTATGTTAATGTTAAAACCATTTTGTTTTAATTTAAAGTCTTTTTCTCTTTTAAGAT
CTTTTTCTATGAAATTTTTTGAACTTATTAAAATACAAATTTTGATTAAGTAATTCCATA
CACAAAATGTTACTTTTATTCTTTTGAACATTTAATTCAATATGAAAAAACAGGTTTTTA
GCAAATATTTTGTTAATCGATATAACACCATTTATTGAGTAATAAAATATTTATTCTGAA
AAGAGAATGAGAAA

>g11995.t8 Gene=g11995 Length=124
MSAADKFCSCVCFKRQEINHFNGCKADFDAQLEKAGDLLVIVDFFATWCGPCKMIAPKLE
EFSNTYSDKIVVVKVDVDECEDLAVQYNISSMPTFVFIKKGQQIDSFSGANAEKLEKYIT
QHTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11995.t8 CDD cd02947 TRX_family 26 119 1.9348E-27
7 g11995.t8 Gene3D G3DSA:3.40.30.10 Glutaredoxin 13 124 1.4E-35
2 g11995.t8 PANTHER PTHR46115 THIOREDOXIN-LIKE PROTEIN 1 26 124 2.5E-44
4 g11995.t8 PRINTS PR00421 Thioredoxin family signature 40 48 5.3E-8
3 g11995.t8 PRINTS PR00421 Thioredoxin family signature 48 57 5.3E-8
5 g11995.t8 PRINTS PR00421 Thioredoxin family signature 88 99 5.3E-8
1 g11995.t8 Pfam PF00085 Thioredoxin 25 120 4.0E-33
9 g11995.t8 ProSitePatterns PS00194 Thioredoxin family active site. 41 59 -
11 g11995.t8 ProSiteProfiles PS51352 Thioredoxin domain profile. 1 124 12.998
6 g11995.t8 SUPERFAMILY SSF52833 Thioredoxin-like 25 122 2.65E-35
10 g11995.t8 TIGRFAM TIGR01068 thioredoxin: thioredoxin 29 122 9.5E-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