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.t4 TSS g1673.t4 12382200 12382200
chr_3 g1673 g1673.t4 isoform g1673.t4 12382274 12384011
chr_3 g1673 g1673.t4 exon g1673.t4.exon1 12382274 12382427
chr_3 g1673 g1673.t4 cds g1673.t4.CDS1 12382274 12382427
chr_3 g1673 g1673.t4 exon g1673.t4.exon2 12382489 12382761
chr_3 g1673 g1673.t4 cds g1673.t4.CDS2 12382489 12382761
chr_3 g1673 g1673.t4 exon g1673.t4.exon3 12383051 12383790
chr_3 g1673 g1673.t4 cds g1673.t4.CDS3 12383051 12383790
chr_3 g1673 g1673.t4 exon g1673.t4.exon4 12383917 12384011
chr_3 g1673 g1673.t4 cds g1673.t4.CDS4 12383917 12383937
chr_3 g1673 g1673.t4 TTS g1673.t4 12384087 12384087

Sequences

>g1673.t4 Gene=g1673 Length=1262
ATGAACCTACAAAGATTGGAAGTTCCATATGTAAATCTATCAACAAACTTTTATAGAAAC
GATCAAAATTTTCAAAGACAGTACTTCCATATCTACGAATCTCGATTAAATTTAATTGGT
GATCTCTTGAAACAAAAAATTTCATCAAAATATGGCAACAAATACCCAATAAAAAAGATT
TCTGAGCTTACTGAAGACAATCCAACAAAATGTATTTTAATCGGAAATCTTTATAAAAAC
ATGGATTTGAAGCCAAGCATTCTGAGGGAAATTGCAGAAGAAAACCAATTAGCTCCATTG
CCTGTTCCACAAGATTTTAATCAGAGCTCGGATGAAATAATTTTAGAAGATAGCATTCAG
CGTATAAAATTATCAGGAAAAATTAATCCTGCTGAACTTGTCACTGGCATCGTTTCTGCC
GTTTTAGGATACAGTGAAGGAGCTGGGAAATTTTACGTTGATGAAATGATTTTCTATGAA
TGTGGAGTTGAGAGACCGCTCAAAGTTATCGACAATTCACCACTTGTTGTCTTTATTTCG
GGAATCGATATGGCTAATATTGATGCACCAATCTTGTCTTTGGATCTATTTCAACAATGG
ATTTATGGAAATTTAGAAATGTCAAGTCGTACAAATTTCGATCCAAAGAATGTTGTTCGT
GTTGTCATAGCTGGAAATTCAACAAGAGCTTGTCCGCCAAAAAAACCTAAAAACGTGAAT
TCTGTAAATTTGAGAATGATTGATACTAAAGGGATGGTTGAGAGTTTGAAAAATTTCGAT
GAAGCTCTTTATCACTTGACTCAATCAGTGTCAGTTGATTTAATGCCTGGTGAATTTGAT
CCAGCAAATTTAATGTTACCTCAACAACCATTTCATCATTGTCTCTTTCCTAAAAGTTCT
GTTAATCGTGGATTAACTGCTGTTCCAAATCCATATCAATTTCAAATTGAAGACCGTTTG
ATATTAGGCACATCTGGACAGAATATTAAGGATATAATGAAATTCTCTACAATGGATGAT
CCACTTGAGTGTATGAAGAATACATTGCGATGGTCTCATTTAGCTCCAACTTGTCCAGAC
ACTCTTCCATGTTATCCTTATTACGATCAAGATCCGTTTATTATTGATGAATGTCCACAC
GTTTATTTTGCAGCACATGATTCAAATTTCAAAAATCTCAATCTATAGCTATCGTCAACA
TGAATACTTTAGAATGTGACGGAATGTCTTTTTCAACAAAAATAGATTTAGAAGAAGAAT
AG

>g1673.t4 Gene=g1673 Length=395
MNLQRLEVPYVNLSTNFYRNDQNFQRQYFHIYESRLNLIGDLLKQKISSKYGNKYPIKKI
SELTEDNPTKCILIGNLYKNMDLKPSILREIAEENQLAPLPVPQDFNQSSDEIILEDSIQ
RIKLSGKINPAELVTGIVSAVLGYSEGAGKFYVDEMIFYECGVERPLKVIDNSPLVVFIS
GIDMANIDAPILSLDLFQQWIYGNLEMSSRTNFDPKNVVRVVIAGNSTRACPPKKPKNVN
SVNLRMIDTKGMVESLKNFDEALYHLTQSVSVDLMPGEFDPANLMLPQQPFHHCLFPKSS
VNRGLTAVPNPYQFQIEDRLILGTSGQNIKDIMKFSTMDDPLECMKNTLRWSHLAPTCPD
TLPCYPYYDQDPFIIDECPHVYFAAHDSNFKNLNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g1673.t4 Gene3D G3DSA:2.40.50.430 - 33 157 0
4 g1673.t4 Gene3D G3DSA:3.60.21.50 - 158 393 0
3 g1673.t4 PANTHER PTHR10416 DNA POLYMERASE DELTA SUBUNIT 2 3 391 0
1 g1673.t4 Pfam PF18018 DNA polymerase delta subunit OB-fold domain 27 155 0
2 g1673.t4 Pfam PF04042 DNA polymerase alpha/epsilon subunit B 176 386 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

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