Gene loci information

Transcript annotation

  • This transcript has been annotated as N-glycosylase/DNA lyase.

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 g9565 g9565.t1 TTS g9565.t1 4068092 4068092
chr_1 g9565 g9565.t1 isoform g9565.t1 4068115 4069130
chr_1 g9565 g9565.t1 exon g9565.t1.exon1 4068115 4068994
chr_1 g9565 g9565.t1 cds g9565.t1.CDS1 4068115 4068994
chr_1 g9565 g9565.t1 exon g9565.t1.exon2 4069051 4069130
chr_1 g9565 g9565.t1 cds g9565.t1.CDS2 4069051 4069130
chr_1 g9565 g9565.t1 TSS g9565.t1 NA NA

Sequences

>g9565.t1 Gene=g9565 Length=960
ATGTCTCTTATTCAAGGAATAATCAAACTTAAATGGCCATTGAGTTTAGAAAGAACGTTA
TTAGGTGGTCAATCATTCAGATTCGTGAAAAATGAAAATGAAGATCATTATATTGGTGTA
TATGCAAATATTCTTTGGAAAATGAAGACAAAAGAAAAGGAATTACATTTTGAAGTTATT
GGAGAATTAAAAGCACCAAATACTAATAAATCAACTTATTATAAAACTCTTCTCACAAAT
TATTTTCGACTGAATGAAGATTTAAATGGAGATTACGAGAAATGGAAGAAAGCACATGAA
CATTTTGATAGTAAAAAAGTAACTGATGTTGCACTTGTAACACAATTAGATCAAGAAGTG
GTGGAAACAGTTTTCAGTTTTATTTGTTCACAAAATAACAATATAAAGCGTATTTCATCG
CTTGTTGAAAAGCTCTGTGTTAATTTTGGAGAAAAAATTTGTAAATTCGAGGACAAGGAT
TATTATTCATTTCCAACTTTGGAAGCATTATCAAAAGAATCAGTTGAAACTAAGTTGCGT
GAACTTGGTTTTGGTTATCGTTCAAAATACATACAAAAGGCTGCAGAAGAAATTATTTCA
AAAGGTGGTGTGGAGTGGCTAGAGAAATTAAAATTAATGAAGTATGAAGATGCTCATAGT
GAATTGTTGAAATTAAGTGGCATAGGACCAAAAGTAGCTGATTGTATTTGCCTCATGTGT
TTAAATTTCCTTCAAGCAGTACCCGTTGACACCCATGTAAAAAAAATTGCATTACATTAT
GTGCCAGAATTAAAGAATTTTAAATCAATGAATATGACTATGTATCGAAAAATTGGAAAT
ACTTTTAGACAAATATATGGCGATAAGTCAGGAGTTGCACAAACAGTTTTATTTTGTAAA
GAATTAACTATTTTTGAGAATGAAGAGAAAGTTATTAAAAAGAAGCCAAAAAAGTCATGA

>g9565.t1 Gene=g9565 Length=319
MSLIQGIIKLKWPLSLERTLLGGQSFRFVKNENEDHYIGVYANILWKMKTKEKELHFEVI
GELKAPNTNKSTYYKTLLTNYFRLNEDLNGDYEKWKKAHEHFDSKKVTDVALVTQLDQEV
VETVFSFICSQNNNIKRISSLVEKLCVNFGEKICKFEDKDYYSFPTLEALSKESVETKLR
ELGFGYRSKYIQKAAEEIISKGGVEWLEKLKLMKYEDAHSELLKLSGIGPKVADCICLMC
LNFLQAVPVDTHVKKIALHYVPELKNFKSMNMTMYRKIGNTFRQIYGDKSGVAQTVLFCK
ELTIFENEEKVIKKKPKKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g9565.t1 CDD cd00056 ENDO3c 122 270 0
10 g9565.t1 Gene3D G3DSA:3.30.310.40 - 5 82 0
9 g9565.t1 Gene3D G3DSA:1.10.1670.10 - 92 302 0
8 g9565.t1 Gene3D G3DSA:1.10.340.30 Hypothetical protein; domain 2 119 243 0
3 g9565.t1 PANTHER PTHR10242:SF2 N-GLYCOSYLASE/DNA LYASE 14 316 0
4 g9565.t1 PANTHER PTHR10242 8-OXOGUANINE DNA GLYCOSYLASE 14 316 0
2 g9565.t1 Pfam PF07934 8-oxoguanine DNA glycosylase, N-terminal domain 14 123 0
1 g9565.t1 Pfam PF00730 HhH-GPD superfamily base excision DNA repair protein 126 260 0
7 g9565.t1 SMART SM00478 endo3end 129 301 0
6 g9565.t1 SUPERFAMILY SSF55945 TATA-box binding protein-like 11 104 0
5 g9565.t1 SUPERFAMILY SSF48150 DNA-glycosylase 120 300 0

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:0006284 base-excision repair BP
GO:0006281 DNA repair BP
GO:0003684 damaged DNA binding MF
GO:0003824 catalytic activity MF
GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity MF
GO:0006289 nucleotide-excision repair 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