General information for g1673.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t2 | TSS | g1673.t2 | 12382200 | 12382200 |
| chr_3 | g1673 | g1673.t2 | isoform | g1673.t2 | 12382274 | 12383400 |
| chr_3 | g1673 | g1673.t2 | exon | g1673.t2.exon1 | 12382274 | 12382427 |
| chr_3 | g1673 | g1673.t2 | cds | g1673.t2.CDS1 | 12382274 | 12382427 |
| chr_3 | g1673 | g1673.t2 | exon | g1673.t2.exon2 | 12382489 | 12382761 |
| chr_3 | g1673 | g1673.t2 | cds | g1673.t2.CDS2 | 12382489 | 12382761 |
| chr_3 | g1673 | g1673.t2 | exon | g1673.t2.exon3 | 12383051 | 12383400 |
| chr_3 | g1673 | g1673.t2 | cds | g1673.t2.CDS3 | 12383051 | 12383400 |
| chr_3 | g1673 | g1673.t2 | TTS | g1673.t2 | 12384087 | 12384087 |
Sequences
>g1673.t2 Gene=g1673 Length=777
ATGAACCTACAAAGATTGGAAGTTCCATATGTAAATCTATCAACAAACTTTTATAGAAAC
GATCAAAATTTTCAAAGACAGTACTTCCATATCTACGAATCTCGATTAAATTTAATTGGT
GATCTCTTGAAACAAAAAATTTCATCAAAATATGGCAACAAATACCCAATAAAAAAGATT
TCTGAGCTTACTGAAGACAATCCAACAAAATGTATTTTAATCGGAAATCTTTATAAAAAC
ATGGATTTGAAGCCAAGCATTCTGAGGGAAATTGCAGAAGAAAACCAATTAGCTCCATTG
CCTGTTCCACAAGATTTTAATCAGAGCTCGGATGAAATAATTTTAGAAGATAGCATTCAG
CGTATAAAATTATCAGGAAAAATTAATCCTGCTGAACTTGTCACTGGCATCGTTTCTGCC
GTTTTAGGATACAGTGAAGGAGCTGGGAAATTTTACGTTGATGAAATGATTTTCTATGAA
TGTGGAGTTGAGAGACCGCTCAAAGTTATCGACAATTCACCACTTGTTGTCTTTATTTCG
GGAATCGATATGGCTAATATTGATGCACCAATCTTGTCTTTGGATCTATTTCAACAATGG
ATTTATGGAAATTTAGAAATGTCAAGTCGTACAAATTTCGATCCAAAGAATGTTGTTCGT
GTTGTCATAGCTGGAAATTCAACAAGAGCTTGTCCGCCAAAAAAACCTAAAAACGTGAAT
TCTGTAAATTTGAGAATGATTGATACTAAAGGGATGGTTGAGAGTTTGAAAAATTTC
>g1673.t2 Gene=g1673 Length=259
MNLQRLEVPYVNLSTNFYRNDQNFQRQYFHIYESRLNLIGDLLKQKISSKYGNKYPIKKI
SELTEDNPTKCILIGNLYKNMDLKPSILREIAEENQLAPLPVPQDFNQSSDEIILEDSIQ
RIKLSGKINPAELVTGIVSAVLGYSEGAGKFYVDEMIFYECGVERPLKVIDNSPLVVFIS
GIDMANIDAPILSLDLFQQWIYGNLEMSSRTNFDPKNVVRVVIAGNSTRACPPKKPKNVN
SVNLRMIDTKGMVESLKNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g1673.t2 | Gene3D | G3DSA:2.40.50.430 | - | 33 | 157 | 0.0e+00 |
| 3 | g1673.t2 | Gene3D | G3DSA:3.60.21.50 | - | 158 | 259 | 2.1e-06 |
| 2 | g1673.t2 | PANTHER | PTHR10416 | DNA POLYMERASE DELTA SUBUNIT 2 | 3 | 233 | 0.0e+00 |
| 1 | g1673.t2 | Pfam | PF18018 | DNA polymerase delta subunit OB-fold domain | 27 | 155 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
