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.t3 TSS g1673.t3 12382200 12382200
chr_3 g1673 g1673.t3 isoform g1673.t3 12382274 12384011
chr_3 g1673 g1673.t3 exon g1673.t3.exon1 12382274 12382427
chr_3 g1673 g1673.t3 exon g1673.t3.exon2 12382489 12384011
chr_3 g1673 g1673.t3 cds g1673.t3.CDS1 12383029 12383856
chr_3 g1673 g1673.t3 TTS g1673.t3 12384087 12384087

Sequences

>g1673.t3 Gene=g1673 Length=1677
ATGAACCTACAAAGATTGGAAGTTCCATATGTAAATCTATCAACAAACTTTTATAGAAAC
GATCAAAATTTTCAAAGACAGTACTTCCATATCTACGAATCTCGATTAAATTTAATTGGT
GATCTCTTGAAACAAAAAATTTCATCAAAATATGGCAACAAATACCCAATAAAAAAGATT
TCTGAGCTTACTGAAGACAATCCAACAAAATGTATTTTAATCGGAAATCTTTATAAAAAC
ATGGATTTGAAGCCAAGCATTCTGAGGGAAATTGCAGAAGAAAACCAATTAGCTCCATTG
CCTGTTCCACAAGATTTTAATCAGAGCTCGGATGAAATAATTTTAGAAGATAGCATTCAG
CGTATAAAATTATCAGGAAAAATTAATCCTGCTGAACTTGTCACTGGCATCGTTTCTGCC
GTTTTAGGTATGAATTATAAATTATGATTCCTTTAAAAATTTTATTGAAAAACAATATTT
AAATAATTATTCTTCCCCATAATATTAATTTCTCAGGAAGAGATCGTAAGTCAAAACTCA
ATCAATAACTTTTTTTATAAATCTAACTTTCATTTATTGAATTCGGTTTTCATTTACTCA
CTACCTTATGATTTTCACTTGTATATATTTGCACAGCTAAATTTTATTTTTCATCTTTGT
TGGGTGTCTTAGAAAGTTATGTCATAAAATATTAATGAGGTTTTTATACATTTTAGGATA
CAGTGAAGGAGCTGGGAAATTTTACGTTGATGAAATGATTTTCTATGAATGTGGAGTTGA
GAGACCGCTCAAAGTTATCGACAATTCACCACTTGTTGTCTTTATTTCGGGAATCGATAT
GGCTAATATTGATGCACCAATCTTGTCTTTGGATCTATTTCAACAATGGATTTATGGAAA
TTTAGAAATGTCAAGTCGTACAAATTTCGATCCAAAGAATGTTGTTCGTGTTGTCATAGC
TGGAAATTCAACAAGAGCTTGTCCGCCAAAAAAACCTAAAAACGTGAATTCTGTAAATTT
GAGAATGATTGATACTAAAGGGATGGTTGAGAGTTTGAAAAATTTCGATGAAGCTCTTTA
TCACTTGACTCAATCAGTGTCAGTTGATTTAATGCCTGGTGAATTTGATCCAGCAAATTT
AATGTTACCTCAACAACCATTTCATCATTGTCTCTTTCCTAAAAGTTCTGTTAATCGTGG
ATTAACTGCTGTTCCAAATCCATATCAATTTCAAATTGAAGACCGTTTGATATTAGGCAC
ATCTGGACAGAATATTAAGGATATAATGAAATTCTCTACAATGGATGATCCACTTGAGTG
TATGAAGAATACATTGCGATGGTCTCATTTAGCTCCAACTTGTCCAGACACTCTTCCATG
TTATCCTTATTACGATCAAGATCCGTTTATTATTGATGAATGTCCACACGTTTATTTTGC
AGCACATGATTCAAATGTACTGCTTACAGAGATTTTTGAAAGTAAGTTCAAATTATATTT
CTTTAAAAAATCTATTTTATAATTTATTCATTAAATTTAGATTCAAATGGTCAAAGAATA
CGACTTCTATGTATTCCATCATTTCAAAAATCTCAATCTATAGCTATCGTCAACATGAAT
ACTTTAGAATGTGACGGAATGTCTTTTTCAACAAAAATAGATTTAGAAGAAGAATAG

>g1673.t3 Gene=g1673 Length=275
MRFLYILGYSEGAGKFYVDEMIFYECGVERPLKVIDNSPLVVFISGIDMANIDAPILSLD
LFQQWIYGNLEMSSRTNFDPKNVVRVVIAGNSTRACPPKKPKNVNSVNLRMIDTKGMVES
LKNFDEALYHLTQSVSVDLMPGEFDPANLMLPQQPFHHCLFPKSSVNRGLTAVPNPYQFQ
IEDRLILGTSGQNIKDIMKFSTMDDPLECMKNTLRWSHLAPTCPDTLPCYPYYDQDPFII
DECPHVYFAAHDSNVLLTEIFESKFKLYFFKKSIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g1673.t3 Gene3D G3DSA:3.60.21.50 - 20 265 0
2 g1673.t3 PANTHER PTHR10416 DNA POLYMERASE DELTA SUBUNIT 2 6 253 0
1 g1673.t3 Pfam PF04042 DNA polymerase alpha/epsilon subunit B 41 251 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