Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase delta subunit 2.

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_3 g1673 g1673.t8 TSS g1673.t8 12382200 12382200
chr_3 g1673 g1673.t8 isoform g1673.t8 12382274 12384011
chr_3 g1673 g1673.t8 exon g1673.t8.exon1 12382274 12382761
chr_3 g1673 g1673.t8 cds g1673.t8.CDS1 12382575 12382761
chr_3 g1673 g1673.t8 exon g1673.t8.exon2 12383051 12383815
chr_3 g1673 g1673.t8 cds g1673.t8.CDS2 12383051 12383815
chr_3 g1673 g1673.t8 exon g1673.t8.exon3 12383875 12384011
chr_3 g1673 g1673.t8 cds g1673.t8.CDS3 12383875 12384011
chr_3 g1673 g1673.t8 TTS g1673.t8 12384087 12384087

Sequences

>g1673.t8 Gene=g1673 Length=1390
ATGAACCTACAAAGATTGGAAGTTCCATATGTAAATCTATCAACAAACTTTTATAGAAAC
GATCAAAATTTTCAAAGACAGTACTTCCATATCTACGAATCTCGATTAAATTTAATTGGT
GATCTCTTGAAACAAAAAATTTCATCAAAATATGGTAAGTATTTAGTTTTTCAAGCCTAA
TGATAAGTTATTTTAGTGATTATTATTCATTTAAGGCAACAAATACCCAATAAAAAAGAT
TTCTGAGCTTACTGAAGACAATCCAACAAAATGTATTTTAATCGGAAATCTTTATAAAAA
CATGGATTTGAAGCCAAGCATTCTGAGGGAAATTGCAGAAGAAAACCAATTAGCTCCATT
GCCTGTTCCACAAGATTTTAATCAGAGCTCGGATGAAATAATTTTAGAAGATAGCATTCA
GCGTATAAAATTATCAGGAAAAATTAATCCTGCTGAACTTGTCACTGGCATCGTTTCTGC
CGTTTTAGGATACAGTGAAGGAGCTGGGAAATTTTACGTTGATGAAATGATTTTCTATGA
ATGTGGAGTTGAGAGACCGCTCAAAGTTATCGACAATTCACCACTTGTTGTCTTTATTTC
GGGAATCGATATGGCTAATATTGATGCACCAATCTTGTCTTTGGATCTATTTCAACAATG
GATTTATGGAAATTTAGAAATGTCAAGTCGTACAAATTTCGATCCAAAGAATGTTGTTCG
TGTTGTCATAGCTGGAAATTCAACAAGAGCTTGTCCGCCAAAAAAACCTAAAAACGTGAA
TTCTGTAAATTTGAGAATGATTGATACTAAAGGGATGGTTGAGAGTTTGAAAAATTTCGA
TGAAGCTCTTTATCACTTGACTCAATCAGTGTCAGTTGATTTAATGCCTGGTGAATTTGA
TCCAGCAAATTTAATGTTACCTCAACAACCATTTCATCATTGTCTCTTTCCTAAAAGTTC
TGTTAATCGTGGATTAACTGCTGTTCCAAATCCATATCAATTTCAAATTGAAGACCGTTT
GATATTAGGCACATCTGGACAGAATATTAAGGATATAATGAAATTCTCTACAATGGATGA
TCCACTTGAGTGTATGAAGAATACATTGCGATGGTCTCATTTAGCTCCAACTTGTCCAGA
CACTCTTCCATGTTATCCTTATTACGATCAAGATCCGTTTATTATTGATGAATGTCCACA
CGTTTATTTTGCAGCACATGATTCAAATGTACTGCTTACAGAGATTTTTGAAAATTCAAA
TGGTCAAAGAATACGACTTCTATGTATTCCATCATTTCAAAAATCTCAATCTATAGCTAT
CGTCAACATGAATACTTTAGAATGTGACGGAATGTCTTTTTCAACAAAAATAGATTTAGA
AGAAGAATAG

>g1673.t8 Gene=g1673 Length=362
MDLKPSILREIAEENQLAPLPVPQDFNQSSDEIILEDSIQRIKLSGKINPAELVTGIVSA
VLGYSEGAGKFYVDEMIFYECGVERPLKVIDNSPLVVFISGIDMANIDAPILSLDLFQQW
IYGNLEMSSRTNFDPKNVVRVVIAGNSTRACPPKKPKNVNSVNLRMIDTKGMVESLKNFD
EALYHLTQSVSVDLMPGEFDPANLMLPQQPFHHCLFPKSSVNRGLTAVPNPYQFQIEDRL
ILGTSGQNIKDIMKFSTMDDPLECMKNTLRWSHLAPTCPDTLPCYPYYDQDPFIIDECPH
VYFAAHDSNVLLTEIFENSNGQRIRLLCIPSFQKSQSIAIVNMNTLECDGMSFSTKIDLE
EE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g1673.t8 Gene3D G3DSA:2.40.50.430 - 1 77 0
4 g1673.t8 Gene3D G3DSA:3.60.21.50 - 78 362 0
3 g1673.t8 PANTHER PTHR10416 DNA POLYMERASE DELTA SUBUNIT 2 1 354 0
1 g1673.t8 Pfam PF18018 DNA polymerase delta subunit OB-fold domain 1 75 0
2 g1673.t8 Pfam PF04042 DNA polymerase alpha/epsilon subunit B 96 306 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:0003677 DNA binding MF
GO:0006260 DNA replication BP

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