General information for g8649.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA polymerase epsilon subunit 3.
Parent gene
- The parent gene g8649 is located on chr_2: 32084542..32085315 (- 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_2 | g8649 | g8649.t4 | TTS | g8649.t4 | 32084450 | 32084450 |
| chr_2 | g8649 | g8649.t4 | isoform | g8649.t4 | 32084542 | 32085315 |
| chr_2 | g8649 | g8649.t4 | exon | g8649.t4.exon1 | 32084542 | 32084780 |
| chr_2 | g8649 | g8649.t4 | cds | g8649.t4.CDS1 | 32084542 | 32084780 |
| chr_2 | g8649 | g8649.t4 | exon | g8649.t4.exon2 | 32084840 | 32085201 |
| chr_2 | g8649 | g8649.t4 | cds | g8649.t4.CDS2 | 32084840 | 32084999 |
| chr_2 | g8649 | g8649.t4 | exon | g8649.t4.exon3 | 32085288 | 32085315 |
| chr_2 | g8649 | g8649.t4 | TSS | g8649.t4 | 32085325 | 32085325 |
Sequences
>g8649.t4 Gene=g8649 Length=629
CTAGTGATGATGGCATTTGAATAGATTCTATAACACCAAACACACTTTTGAGACCTATAA
ACTTTTAGTTAAAGCGAATAATAAAATTTAAAATATTCGTCTTTCTTGAAATTTTCCACG
ATCTTAAAACTTGATCTTAAAAATTAGTTCAGTTTGAACTTGATTGATCTTAAATTTTTG
TAAACAAGTAGTTCAAGAGTGAATTTAAAAAATAATAAATAAAAATAAAAATGTCCGCAG
CAGATGAGAAAATTAGTGATTTACAATTGCCAATTGCTTCTGTAGCTCGCTTAATTAAGG
AAGCCTTACCAAATGGAGCAATAGCAAAACAAGAAGCTAAATTAGCGATTGCTCGAGCTG
CAAGTGTTTTTGTTCTTTTTCTTACAAGCGCTACAATAGATGTGACTACTTCATCCAATC
AAAAAACTTTGATGGCTCAGCATGTATTTAACGCATTAAAAGAAATTGAATTCGAAATGT
TTTTGCCTGAACTTCAAAAAAGTTTAGAAACATACAGACAAGCTATGAAAAACAAAAAAG
ATCGAAAATCAATCAATGATGCAAGTGAAAATAACACTGAAAATCAAATAGAAGATGAAG
AAGATGTGATTCAGATTGATGATGATTAA
>g8649.t4 Gene=g8649 Length=132
MSAADEKISDLQLPIASVARLIKEALPNGAIAKQEAKLAIARAASVFVLFLTSATIDVTT
SSNQKTLMAQHVFNALKEIEFEMFLPELQKSLETYRQAMKNKKDRKSINDASENNTENQI
EDEEDVIQIDDD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8649.t4 | Coils | Coil | Coil | 85 | 105 | - |
| 6 | g8649.t4 | Gene3D | G3DSA:1.10.20.10 | Histone | 2 | 131 | 5.9E-32 |
| 4 | g8649.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 100 | 132 | - |
| 5 | g8649.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 132 | - |
| 2 | g8649.t4 | PANTHER | PTHR46172 | DNA POLYMERASE EPSILON SUBUNIT 3 | 2 | 122 | 2.6E-28 |
| 1 | g8649.t4 | Pfam | PF00808 | Histone-like transcription factor (CBF/NF-Y) and archaeal histone | 12 | 76 | 2.9E-12 |
| 3 | g8649.t4 | SUPERFAMILY | SSF47113 | Histone-fold | 10 | 126 | 1.19E-28 |
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:0046982 | protein heterodimerization activity | MF |
KEGG
Orthology
- This transcript has been annotated with K02326 (DNA polymerase epsilon subunit 3)
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.
