Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Single-strand selective monofunctional uracil DNA glycosylase.

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_2 g5636 g5636.t1 TSS g5636.t1 10784055 10784055
chr_2 g5636 g5636.t1 isoform g5636.t1 10784125 10785101
chr_2 g5636 g5636.t1 exon g5636.t1.exon1 10784125 10784413
chr_2 g5636 g5636.t1 cds g5636.t1.CDS1 10784125 10784413
chr_2 g5636 g5636.t1 exon g5636.t1.exon2 10784466 10784767
chr_2 g5636 g5636.t1 cds g5636.t1.CDS2 10784466 10784767
chr_2 g5636 g5636.t1 exon g5636.t1.exon3 10784826 10785101
chr_2 g5636 g5636.t1 cds g5636.t1.CDS3 10784826 10785101
chr_2 g5636 g5636.t1 TTS g5636.t1 10785325 10785325

Sequences

>g5636.t1 Gene=g5636 Length=867
ATGAATCGACAACATTCAGAAGATTTAGAAAATGATGAAGAGAATAATGAAGAACAACAG
GATAAAGAAGACATTTTAAGGAAATTATCAGTTGATATTACATTTGAAAAATCATTTTGG
GAAAAAATCGACGCAATTGAGAATGAATTAGTTAGTGAATTATTGGAAATAGACTTTCTG
AAAGATAATAACGTCGATGCTGTTTATAATCCACTTGATTATGCTGCGGATATTCATATT
AATTACTTGAAGAAATTTTTGAAACAATCTCCTTCAGTTTTATTCTTAGGCATGAATCCT
GGTCTTTTGGGTATGTGTCAAACTGGTGTGCCTTTCGGAAATGTTTCGTCAGTTAAAAAT
TGGATGAAATTGAGTGGTAAAGTTGAGAAACCAAAAATTGAGATTAAAATGAAACCAATC
GAAGGATTAGAGTGTAAAAAAGAAGAACAAAGTGGAAAACGATTTTGGGGATTGATGGAA
GAACTTTGTGGAGAACCTGAAAATTTCTTTCGTCATTGCTTCGTATATAATCTTTGCCCA
CTTGCATTTCTTAGCAAAACTGGTCGCAATATTACACCAACTGAATTAAAGGGTGAATGT
AAGAACGCATTAAACACTGTCTGTTTAAATTATCTTTCAAAAATTATCAACACATTAAAG
CCAAAAGTAATTATCACTGTTGGTTCTTATGCAGAGCAAAAAATCAAAGATTTAAAAAAG
AAAAATCTTATTTCTGAATCAATCGAGTGTAAGTTACTTCCACATCCATCACCACGAGCA
CTAAATAATAATGATTGGGTTGAAAAAGCACGCAAATGGATGCGTGAAAATGACATGCTT
AAATATTTCAAAACAGAACAATCGTAA

>g5636.t1 Gene=g5636 Length=288
MNRQHSEDLENDEENNEEQQDKEDILRKLSVDITFEKSFWEKIDAIENELVSELLEIDFL
KDNNVDAVYNPLDYAADIHINYLKKFLKQSPSVLFLGMNPGLLGMCQTGVPFGNVSSVKN
WMKLSGKVEKPKIEIKMKPIEGLECKKEEQSGKRFWGLMEELCGEPENFFRHCFVYNLCP
LAFLSKTGRNITPTELKGECKNALNTVCLNYLSKIINTLKPKVIITVGSYAEQKIKDLKK
KNLISESIECKLLPHPSPRALNNNDWVEKARKWMRENDMLKYFKTEQS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5636.t1 CDD cd19374 UDG-F3_SMUG1-like 41 276 9.20641E-110
6 g5636.t1 Coils Coil Coil 2 29 -
7 g5636.t1 Coils Coil Coil 43 63 -
5 g5636.t1 Gene3D G3DSA:3.40.470.10 - 37 285 1.7E-90
4 g5636.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 23 -
2 g5636.t1 PANTHER PTHR13235 SINGLE-STRAND SELECTIVE MONOFUNCTIONAL URACIL DNA GLYCOSYLASE 34 285 1.3E-73
1 g5636.t1 Pfam PF03167 Uracil DNA glycosylase superfamily 150 273 2.5E-10
3 g5636.t1 SUPERFAMILY SSF52141 Uracil-DNA glycosylase-like 38 275 3.66E-50

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5636/g5636.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5636.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0017065 single-strand selective uracil DNA N-glycosylase activity MF
GO:0006284 base-excision repair BP

KEGG

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