General information for g1673.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA polymerase delta subunit 2.
Parent gene
- The parent gene g1673 is located on chr_3: 12382784..12384011 (+ strand)
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.t9 | TSS | g1673.t9 | 12382200 | 12382200 |
| chr_3 | g1673 | g1673.t9 | isoform | g1673.t9 | 12382784 | 12384011 |
| chr_3 | g1673 | g1673.t9 | exon | g1673.t9.exon1 | 12382784 | 12383815 |
| chr_3 | g1673 | g1673.t9 | cds | g1673.t9.CDS1 | 12383029 | 12383815 |
| chr_3 | g1673 | g1673.t9 | exon | g1673.t9.exon2 | 12383875 | 12384011 |
| chr_3 | g1673 | g1673.t9 | cds | g1673.t9.CDS2 | 12383875 | 12384011 |
| chr_3 | g1673 | g1673.t9 | TTS | g1673.t9 | 12384087 | 12384087 |
Sequences
>g1673.t9 Gene=g1673 Length=1169
CCTTTAAAAATTTTATTGAAAAACAATATTTAAATAATTATTCTTCCCCATAATATTAAT
TTCTCAGGAAGAGATCGTAAGTCAAAACTCAATCAATAACTTTTTTTATAAATCTAACTT
TCATTTATTGAATTCGGTTTTCATTTACTCACTACCTTATGATTTTCACTTGTATATATT
TGCACAGCTAAATTTTATTTTTCATCTTTGTTGGGTGTCTTAGAAAGTTATGTCATAAAA
TATTAATGAGGTTTTTATACATTTTAGGATACAGTGAAGGAGCTGGGAAATTTTACGTTG
ATGAAATGATTTTCTATGAATGTGGAGTTGAGAGACCGCTCAAAGTTATCGACAATTCAC
CACTTGTTGTCTTTATTTCGGGAATCGATATGGCTAATATTGATGCACCAATCTTGTCTT
TGGATCTATTTCAACAATGGATTTATGGAAATTTAGAAATGTCAAGTCGTACAAATTTCG
ATCCAAAGAATGTTGTTCGTGTTGTCATAGCTGGAAATTCAACAAGAGCTTGTCCGCCAA
AAAAACCTAAAAACGTGAATTCTGTAAATTTGAGAATGATTGATACTAAAGGGATGGTTG
AGAGTTTGAAAAATTTCGATGAAGCTCTTTATCACTTGACTCAATCAGTGTCAGTTGATT
TAATGCCTGGTGAATTTGATCCAGCAAATTTAATGTTACCTCAACAACCATTTCATCATT
GTCTCTTTCCTAAAAGTTCTGTTAATCGTGGATTAACTGCTGTTCCAAATCCATATCAAT
TTCAAATTGAAGACCGTTTGATATTAGGCACATCTGGACAGAATATTAAGGATATAATGA
AATTCTCTACAATGGATGATCCACTTGAGTGTATGAAGAATACATTGCGATGGTCTCATT
TAGCTCCAACTTGTCCAGACACTCTTCCATGTTATCCTTATTACGATCAAGATCCGTTTA
TTATTGATGAATGTCCACACGTTTATTTTGCAGCACATGATTCAAATGTACTGCTTACAG
AGATTTTTGAAAATTCAAATGGTCAAAGAATACGACTTCTATGTATTCCATCATTTCAAA
AATCTCAATCTATAGCTATCGTCAACATGAATACTTTAGAATGTGACGGAATGTCTTTTT
CAACAAAAATAGATTTAGAAGAAGAATAG
>g1673.t9 Gene=g1673 Length=307
MRFLYILGYSEGAGKFYVDEMIFYECGVERPLKVIDNSPLVVFISGIDMANIDAPILSLD
LFQQWIYGNLEMSSRTNFDPKNVVRVVIAGNSTRACPPKKPKNVNSVNLRMIDTKGMVES
LKNFDEALYHLTQSVSVDLMPGEFDPANLMLPQQPFHHCLFPKSSVNRGLTAVPNPYQFQ
IEDRLILGTSGQNIKDIMKFSTMDDPLECMKNTLRWSHLAPTCPDTLPCYPYYDQDPFII
DECPHVYFAAHDSNVLLTEIFENSNGQRIRLLCIPSFQKSQSIAIVNMNTLECDGMSFST
KIDLEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g1673.t9 | Gene3D | G3DSA:3.60.21.50 | - | 20 | 307 | 0 |
| 2 | g1673.t9 | PANTHER | PTHR10416 | DNA POLYMERASE DELTA SUBUNIT 2 | 6 | 299 | 0 |
| 1 | g1673.t9 | 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.
