General information for g9531.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA polymerase epsilon subunit 2.
Parent gene
- The parent gene g9531 is located on chr_1: 3915516..3916934 (+ 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_1 | g9531 | g9531.t1 | TSS | g9531.t1 | 3915142 | 3915142 |
| chr_1 | g9531 | g9531.t1 | isoform | g9531.t1 | 3915222 | 3916934 |
| chr_1 | g9531 | g9531.t1 | exon | g9531.t1.exon1 | 3915222 | 3915440 |
| chr_1 | g9531 | g9531.t1 | cds | g9531.t1.CDS1 | 3915222 | 3915440 |
| chr_1 | g9531 | g9531.t1 | exon | g9531.t1.exon2 | 3915511 | 3916599 |
| chr_1 | g9531 | g9531.t1 | cds | g9531.t1.CDS2 | 3915511 | 3916599 |
| chr_1 | g9531 | g9531.t1 | exon | g9531.t1.exon3 | 3916656 | 3916934 |
| chr_1 | g9531 | g9531.t1 | cds | g9531.t1.CDS3 | 3916656 | 3916934 |
| chr_1 | g9531 | g9531.t1 | TTS | g9531.t1 | 3916953 | 3916953 |
Sequences
>g9531.t1 Gene=g9531 Length=1587
ATGGATATTAATAAAGGAAAAACAGAAATAATAAAATTCTTTAAAATAAGTGGTCTACAA
ATGCGATCTGAAGTCGCTATGGTGCTTTTAGATAAGTACAAAGAAATCAATGATAGCAAA
GAAAGAAGGAAATTTCTTGACAAAATACTGATTAATATACAAAATCAGACAATAAAAAAC
AATTCAATTGAGTTGGAAAACATTAAAATTGCTTTACGAGACACTTCAAATAGAAACGGT
TATAATGAAGAATCTGAACCAATTTTTAGTGTAATAAATGCTTTTGATGTACCATCATTT
GAATATTGCAAAGGCACGAAAAAGTTTATACCAAAAACTACCAAATCTAAGCTTCTTGCT
TCTGCTACATCACGATCGGAATATATACGAAATCGTTACAATACTATTTTACAGAGAATT
TTGAGACATGATCTTTTTGCACCAAATGTGAATGAAAACATTCGATCTTCAGATAATGAA
GTGCGTAAGTTTACGTTAAAATATGCAGAAAATTTAATGTCTGCATCAAGTGTTCCAGAG
GTTGTCATGCTTGGTTTGCTCTCAAAATTTAAAGAAGGAAAGTTCTATTTAGAAGATCCA
ACTGGCGCAATTCCAATTGATTTAAGTGAAACTAAATTTCATAATGGTTTGTACACAGAA
GGTAGTTTTATGCTTGCTGAGGGAAGTTATAATGATGGCATTTTGAAAGTGAATGGACTT
GGATTTCCTCCTATTGAACCGAGCTCAAGCAGTCGTGCCTATTTTGGGACTCAAAATTAT
TTTGGTGGTAGTTCATCTACTTTACTGAAATTCTCAAAAAGACTTCTTGAGTATGAGCGA
TTGAATTTCGGTGCAAGTCTTATATTTCTTGCTGATTGTTGGCTTGATGATGCTGGTGTA
ATGGATAAACTTAAAAAACTATTTATTGGATTTGATGAGTCACCTCCTATAGCAATCATT
TTAATGGGACCATTTCAAAAGAATAAAGGAAATGCTATGTCATTAAGAAGTAGATTTTCA
CAATTAGCTGATTTAATTGATGCAACATTCAATTTAAAAACTGAAACAGATATAGTCTTA
GTACCAGATATTGAAGATCCAACAACTGCTAATATTCTTCCACGTCCATCTTTGCCAACA
TGTATAGTTCAAGATTTACTTAAAAAGAACAAAAGGGTGATTCTTGCTACAAATCCTTGT
CGATTACAATATTGTACACAAGAAATTGTTGTTTGTCGACTCGATTTATTACGAAAGTTA
TGTCGAAATACAATAAAATTTCCTGATTCTGGTCAACTTGCTGATCACTTTGTGCGAACA
CTTTTATGTCAAGGAACATTGGCACCATTTACTCAACTAGTGTTGCCTACATATTGGGAT
TTTGATTCATCATTGAGCTTATATCCACTTCCTGATTTAATTGTCATTGGTGATAATAGT
ACAGATTTTCAGAAAACTCATAATGAATGTAATGTTGTTAATACTGGATCTTTTCCTCGT
TCTAAATATTCATTTAAAGTTTATACACCTAATAATCGAACTGTAGAAGATTCGCAAATA
CCCGATGATGATGATATGGAAAATTAA
>g9531.t1 Gene=g9531 Length=528
MDINKGKTEIIKFFKISGLQMRSEVAMVLLDKYKEINDSKERRKFLDKILINIQNQTIKN
NSIELENIKIALRDTSNRNGYNEESEPIFSVINAFDVPSFEYCKGTKKFIPKTTKSKLLA
SATSRSEYIRNRYNTILQRILRHDLFAPNVNENIRSSDNEVRKFTLKYAENLMSASSVPE
VVMLGLLSKFKEGKFYLEDPTGAIPIDLSETKFHNGLYTEGSFMLAEGSYNDGILKVNGL
GFPPIEPSSSSRAYFGTQNYFGGSSSTLLKFSKRLLEYERLNFGASLIFLADCWLDDAGV
MDKLKKLFIGFDESPPIAIILMGPFQKNKGNAMSLRSRFSQLADLIDATFNLKTETDIVL
VPDIEDPTTANILPRPSLPTCIVQDLLKKNKRVILATNPCRLQYCTQEIVVCRLDLLRKL
CRNTIKFPDSGQLADHFVRTLLCQGTLAPFTQLVLPTYWDFDSSLSLYPLPDLIVIGDNS
TDFQKTHNECNVVNTGSFPRSKYSFKVYTPNNRTVEDSQIPDDDDMEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g9531.t1 | Gene3D | G3DSA:1.10.8.60 | - | 1 | 76 | 1e-07 |
| 3 | g9531.t1 | PANTHER | PTHR12708 | DNA POLYMERASE EPSILON SUBUNIT B | 9 | 519 | 0e+00 |
| 5 | g9531.t1 | PIRSF | PIRSF000799 | DNA_pol_epsilon_2 | 1 | 521 | 0e+00 |
| 1 | g9531.t1 | Pfam | PF12213 | DNA polymerases epsilon N terminal | 7 | 74 | 0e+00 |
| 2 | g9531.t1 | Pfam | PF04042 | DNA polymerase alpha/epsilon subunit B | 288 | 484 | 0e+00 |
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 |
| GO:0006261 | DNA-dependent DNA replication | BP |
| GO:0008622 | epsilon DNA polymerase complex | CC |
KEGG
Orthology
- This transcript has been annotated with K02325 (DNA polymerase epsilon 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.
