General information for g1673.t6
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.t6 | TSS | g1673.t6 | 12382200 | 12382200 |
| chr_3 | g1673 | g1673.t6 | isoform | g1673.t6 | 12382274 | 12384011 |
| chr_3 | g1673 | g1673.t6 | exon | g1673.t6.exon1 | 12382274 | 12382427 |
| chr_3 | g1673 | g1673.t6 | cds | g1673.t6.CDS1 | 12382425 | 12382427 |
| chr_3 | g1673 | g1673.t6 | exon | g1673.t6.exon2 | 12382494 | 12382761 |
| chr_3 | g1673 | g1673.t6 | cds | g1673.t6.CDS2 | 12382494 | 12382761 |
| chr_3 | g1673 | g1673.t6 | exon | g1673.t6.exon3 | 12383051 | 12383815 |
| chr_3 | g1673 | g1673.t6 | cds | g1673.t6.CDS3 | 12383051 | 12383815 |
| chr_3 | g1673 | g1673.t6 | exon | g1673.t6.exon4 | 12383875 | 12384011 |
| chr_3 | g1673 | g1673.t6 | cds | g1673.t6.CDS4 | 12383875 | 12384011 |
| chr_3 | g1673 | g1673.t6 | TTS | g1673.t6 | 12384087 | 12384087 |
Sequences
>g1673.t6 Gene=g1673 Length=1324
ATGAACCTACAAAGATTGGAAGTTCCATATGTAAATCTATCAACAAACTTTTATAGAAAC
GATCAAAATTTTCAAAGACAGTACTTCCATATCTACGAATCTCGATTAAATTTAATTGGT
GATCTCTTGAAACAAAAAATTTCATCAAAATATGAAATACCCAATAAAAAAGATTTCTGA
GCTTACTGAAGACAATCCAACAAAATGTATTTTAATCGGAAATCTTTATAAAAACATGGA
TTTGAAGCCAAGCATTCTGAGGGAAATTGCAGAAGAAAACCAATTAGCTCCATTGCCTGT
TCCACAAGATTTTAATCAGAGCTCGGATGAAATAATTTTAGAAGATAGCATTCAGCGTAT
AAAATTATCAGGAAAAATTAATCCTGCTGAACTTGTCACTGGCATCGTTTCTGCCGTTTT
AGGATACAGTGAAGGAGCTGGGAAATTTTACGTTGATGAAATGATTTTCTATGAATGTGG
AGTTGAGAGACCGCTCAAAGTTATCGACAATTCACCACTTGTTGTCTTTATTTCGGGAAT
CGATATGGCTAATATTGATGCACCAATCTTGTCTTTGGATCTATTTCAACAATGGATTTA
TGGAAATTTAGAAATGTCAAGTCGTACAAATTTCGATCCAAAGAATGTTGTTCGTGTTGT
CATAGCTGGAAATTCAACAAGAGCTTGTCCGCCAAAAAAACCTAAAAACGTGAATTCTGT
AAATTTGAGAATGATTGATACTAAAGGGATGGTTGAGAGTTTGAAAAATTTCGATGAAGC
TCTTTATCACTTGACTCAATCAGTGTCAGTTGATTTAATGCCTGGTGAATTTGATCCAGC
AAATTTAATGTTACCTCAACAACCATTTCATCATTGTCTCTTTCCTAAAAGTTCTGTTAA
TCGTGGATTAACTGCTGTTCCAAATCCATATCAATTTCAAATTGAAGACCGTTTGATATT
AGGCACATCTGGACAGAATATTAAGGATATAATGAAATTCTCTACAATGGATGATCCACT
TGAGTGTATGAAGAATACATTGCGATGGTCTCATTTAGCTCCAACTTGTCCAGACACTCT
TCCATGTTATCCTTATTACGATCAAGATCCGTTTATTATTGATGAATGTCCACACGTTTA
TTTTGCAGCACATGATTCAAATGTACTGCTTACAGAGATTTTTGAAAATTCAAATGGTCA
AAGAATACGACTTCTATGTATTCCATCATTTCAAAAATCTCAATCTATAGCTATCGTCAA
CATGAATACTTTAGAATGTGACGGAATGTCTTTTTCAACAAAAATAGATTTAGAAGAAGA
ATAG
>g1673.t6 Gene=g1673 Length=390
MKYPIKKISELTEDNPTKCILIGNLYKNMDLKPSILREIAEENQLAPLPVPQDFNQSSDE
IILEDSIQRIKLSGKINPAELVTGIVSAVLGYSEGAGKFYVDEMIFYECGVERPLKVIDN
SPLVVFISGIDMANIDAPILSLDLFQQWIYGNLEMSSRTNFDPKNVVRVVIAGNSTRACP
PKKPKNVNSVNLRMIDTKGMVESLKNFDEALYHLTQSVSVDLMPGEFDPANLMLPQQPFH
HCLFPKSSVNRGLTAVPNPYQFQIEDRLILGTSGQNIKDIMKFSTMDDPLECMKNTLRWS
HLAPTCPDTLPCYPYYDQDPFIIDECPHVYFAAHDSNVLLTEIFENSNGQRIRLLCIPSF
QKSQSIAIVNMNTLECDGMSFSTKIDLEEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g1673.t6 | Gene3D | G3DSA:2.40.50.430 | - | 1 | 105 | 0 |
| 4 | g1673.t6 | Gene3D | G3DSA:3.60.21.50 | - | 106 | 390 | 0 |
| 3 | g1673.t6 | PANTHER | PTHR10416 | DNA POLYMERASE DELTA SUBUNIT 2 | 3 | 382 | 0 |
| 1 | g1673.t6 | Pfam | PF18018 | DNA polymerase delta subunit OB-fold domain | 4 | 103 | 0 |
| 2 | g1673.t6 | Pfam | PF04042 | DNA polymerase alpha/epsilon subunit B | 124 | 334 | 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 transcript has been annotated with K02328 (DNA polymerase delta subunit 2)
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. There were no conditions that were differentially expressed