Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase epsilon catalytic subunit 1.

Parent gene

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 g14177 g14177.t1 TTS g14177.t1 35239495 35239495
chr_1 g14177 g14177.t1 isoform g14177.t1 35240399 35247204
chr_1 g14177 g14177.t1 exon g14177.t1.exon1 35240399 35241169
chr_1 g14177 g14177.t1 cds g14177.t1.CDS1 35240399 35241169
chr_1 g14177 g14177.t1 exon g14177.t1.exon2 35241230 35245016
chr_1 g14177 g14177.t1 cds g14177.t1.CDS2 35241230 35245016
chr_1 g14177 g14177.t1 exon g14177.t1.exon3 35245069 35246885
chr_1 g14177 g14177.t1 cds g14177.t1.CDS3 35245069 35246885
chr_1 g14177 g14177.t1 exon g14177.t1.exon4 35246942 35247098
chr_1 g14177 g14177.t1 cds g14177.t1.CDS4 35246942 35247098
chr_1 g14177 g14177.t1 exon g14177.t1.exon5 35247158 35247204
chr_1 g14177 g14177.t1 cds g14177.t1.CDS5 35247158 35247204
chr_1 g14177 g14177.t1 TSS g14177.t1 NA NA

Sequences

>g14177.t1 Gene=g14177 Length=6579
ATGTACAATAAATACAAAGATAATGCTGAAAAGCAATCGCAATTTGGCTTATTGGAAAAT
AACAGTGATGATTTTATGAGTACAAAAGCAGCAGAGCAAAGTTACAAAAACTCGCGAGAA
AATGATTATATTGACTCTAAATATGGCTTTGATAGATTGAAGGACGGTATAGAAAGAACT
GGATATCTTATCAATATGCATTCTACTGACATTCTTGATCATGAAAAACGACTTGTTTCT
GCTCTGGATCTCTATTTTATTACAATGAATGGCTCTAGATTCAAAGTTTCTGTCATATAT
CAACCCTACTTCTTTGTTATAATAGAACAACAGCAAATTTATGAAGTGACAACTTTCTTG
CAACGAAAATACGGAGGTCAAGCATCAAAGATAGAGATAGTTGAGAAAGAAGATCTTGAC
ATGCCTAATCATTTGACTGGGAAGAAACATAGAATGATAAAGCTTTCATTTCACAACACA
ACTGTTATGAACAAAGTTCGAATTGAAATAAATCGTTCAGTTAAAAAGAATAAGGAGCGA
GAAAAATCAAATACATTTTATATGCAAATGCTGTCAATGTCATTAACAGGAAGAACATCA
AATGAACAGATTTATGATTATATGGATTTTATTATGGACATTCGTGAACATGATGTGCCT
TATCACGTTCGAGTTTCAATTGATTTGAAAGTTTTCTGTGGTCTCTGGTATAATATAAAA
GATCGTGGTGCAAATGAATTGCCTTCTATTGTTCAACGACCAGATATTCTTGAACGACCT
GAACCAATTGTTTTAGCTTATGATATAGAAACTACTAAATTACCACTTAAATTCCCAGAT
GCTCAAACTGATCAAATTATGATGATTTCATATATGATTGATGGTCAAGGATATTTAATT
ACAAATCGTGAAATTGTCTCATCTGATGTAGATGATTTTGAATACACACCTAAACCAGAA
TTTGAAGGAAATTTCATAGTTTTTAATGAACCAAATGAGTTATCACTAATTCAACGTTTT
TTCGATCACATACTTGAAGTTCGACCTCATATTATAGTAACATACAATGGAGATTTTTTC
GATTGGCCGTTTGTTGAAACTCGTGCAGCTACTTATGACATTGATATGAAAAGAGAAATT
GGATACAGCAAGAATCGAGAAGGAAATTATCTCTCAAGACCATCCATGCACATGGATTGT
CTTTGTTGGGTAAAACGTGATTCTTATTTACCTGTTGGTTCTCAAGGTCTCAAAGCTGTA
GCTAAAGCAAAATTGCGGTACGATCCTGTTGAATTAGATCCAGAAGAGATGTGCAAAAAA
GCAGTTGAACAACCACAAGAGCTCGCAAGTTATTCAGTTTCAGATGCTGTTGCAACATAT
TATCTTTATATGAAATATGTTCAACCTTTTATTTTTGCTTTGACAACAATTATTCCAATG
GAACCCGATGAAGTTCTTCGTAAAGGTTCTGGAACTCTATGTGAATCGTTGCTGATGAAA
GAAGCATATCATGCCAACATCATTTTTCCAAATAAAGAACAGGCAGAATTAAATAAATTG
ACAGAAGATGGACATATGCTCGATACTGAAACTTATGTTGGTGGTCATATAGAAGCTTTA
GAATCTGGAGTTTTCAGAGCTGATTTACCATACAGATTTCGATTGGATTGTGGTATGCTG
CAAGAATTGAAGAATAAAGTATCACATGTTCTTAAGCATGCAATTGAAGTAGAAGAAAAT
ATTCCATTATCTGAAGTAACTAATTTTGATGAAGTAACAAAACAAATTCAAGATGTTTTA
CAAGCTCTTCATGATAATCCAAATCGAGTTGAAAAACCAGTTATTTATCACTTGGATGTT
GGTGCTATGTATCCAAATATTATCTTAACTAATCGTCTTCAACCATCTGCTATGGTAACT
GAACAGGATTGTGCAGCTTGTGATTTTAATCGACCCGATGCAGCATGCAAGCGTCAAATG
GATTGGTTATGGAGAGGTGAAATACTTCCTGCAACAAGAAGTGAATTTCAACGTATTCAA
CAACAACTTGAGACTGAAAAATTTCCACCACTTGTGCCTGGAGGGCCATATCGAGCTTTT
CATGAATTGTCACGTGAAGATCGTGCTGCAATTGAGAAGAAGCGTTTGAGTGATTATTGT
CGAAAAGCTTATAAAAAGACTAAAATAACAAAGCTCGAAACTAGGACGTCCACAATTTGT
CAAATGGAGAATAGTTTTTATGTTGATACAGTTCGTGCTTTTCGTGATCGACGTTATGAA
TACAAAGGACTCACAAAAGTTGCAAAATCAGAAGTGGCTAAAGCATTGAAATCAGGAGAT
GCGAGTGAAATCAAAGCTGCAAAGGGACGTGAAGTTCTGTATGATTCTCTACAATTGGCC
CACAAATGTATTCTCAATTCATTTTATGGTTATGTCATGAGAAAAGGTGCACGATGGCAT
AGCATGCAAATGGGTGGTATTGTGTGTTTGACAGGATCAAATATCATTACAAAAGCTAGA
GAAGTGATTGAGAAAGTCGGTCGTCCTTTAGAATTAGATACTGATGGTATTTGGTGTATC
TTGCCAGGAACTTTTCCACAAGATTTTGAAGTTTTTACAAATTTACCAAAGAAATCAAAA
ATTACAGTCAGCTATCCAAATGCAGTTCTCAATACTATGGTCAAAGATCACTTTACTAAT
GATCAATATCACAATCTTGATAAATCTGCAGAAAATGGTGAAGTTCCTGAATATTCAATT
CGATCTGAGAACTCTATTTTCTTTGAAGTTGATGGTCCATATTTGGCTATGGTTTTACCT
GCTGCAAAAGAAGAAGGAAAGAAATTAAAGAAACGTTATGCTGTGTTTAATTTTGACGGT
TCATTGGCAGAACTGAAAGGTTTTGAAATCAAACGTCGTGGTGAATTGCAGCTCATTAAA
ATTTTTCAATCACAAGTATTTGAAGCATTTTTACAAGGAAATACACTTGAAAAGTGTTAT
CAATGTGTAGCCAAAGTTGCTAATTATTGGTTAGATGTTCTCTACAGTAAAGGAGCTAAT
ATGCCTGATTCTGAACTTTTTGAATTGATTTCTGAAAATCGTTCAATGTCAAAGAAGCTT
GAAGAATATGGAGAGCAAAAATCCACATCAATTTCAACAGCAAAACGTTTGGCTGAATTT
CTTGGTGATCAAATGGTTAAAGACGCTGGTCTGGCATGTAAATACATAATAAGCAGAAAA
CCAGAAGGAGCACCAGTTACAGAAAGAGCTATACCTTTAGCCATTTTCCAATCAGAATCT
TCTGTACGTCGCTTTCATATTCGTAAATGGTTAAAAGATTCAAATATTGATGGTGATGTT
GATATACGCGATATTCTTGATTGGAATTATTATATCGAACGTATTGGTGGAGCTATACAG
AAAATTATAACAATTCCTGCTGCACTTCAAGGTGTTTCTAATCCTGTGCCTCGTGTTCAA
CATCCAGATTGGTTACATAAAAAAGTTCTTGAGAAAAATGACACATTTAAGCAACGACGA
ATCAATGAGTTATTTAAAGCTACACCCAAACCCATAGCTGAAGTTCGTGATATTGAAGAT
TCTGTTGGAAATAGTCAAAAATCACAAGGTATACCTGTTGTAACTAGTCGAAAACGAACA
AGAACTGAAGAAAATTTTGAAACACAACCAAAAACATGGCGTGAAGCACTTGGCAATCCT
CCCGAAATTGGAACAACTCGCGAAGAATTTGTTAAATGGTTAAAATTTCAAAAAAAGAAA
TGGCGTTTTCAATTGGACCAAAGAAAGAAATTGCGAGGTGATAGTGGAAATAAAAGAGTT
CGTCAAGATGAAGTTCCATTAGTTGACGCAGTTCAACGTGGTCCTATTTCAACACTTGGT
GGCTTTTTAAAGAGAACTCAAAGAAATTTGATTGAATTAACTTGGCAAATTATTCAAATT
GTGCCTTTAGATCTTGATGGACATTTTTACTTGTGGGCAATAATTGGTGATGAATTGCAG
AAGATTAAACTTGATATACCGAGAATATTTTATGTCAATCAACGAACACCTGCACCATCA
TGCGAAAACGAAAACGATAAAATTTCATGGAAAAAAGTTCATCGTGTGTTGCCTCGTTCA
CGTCCAATATTTAATTTATATCAGTATAAAGTGCCTGAACAAGTTTTCCGTGATAATGGT
CTTGGAATGCTTGTTGATTTGGCAGCACCTGATATTGAGGGAATTTATGAAACTCAAATG
AGCTTAGAATTCAGAGCAATTATGCAACTTGGATGTTCTTGTGCAGTACAAAGAGCAGAA
GCTAAAAAAATTGCATCTTCAGTAAATTTACAACGTGACATATTTACACTCGATCAATTA
GAACAAAGAATGCAACTTCATCAACCATATTTGAAAGAAGGTGGGAACATGAAAAAACTC
TTTCTTTATTATCATACAATTCCATCAGGCAAAAAGAGCATGTGGGGATTATTTTTAACA
CCACTCAACAAAGCTGTTATAATTGTTCACGATACAGTTAGAACTAATCAAATGCCAAGT
TTGAGAAACTTGTACACAACTGAAAGACAAGCTCTTCTTTCAAGAGATGATTCGATTAGT
GACAAATTGCCACCAAGTGAAATTCAATTTGATATTCATGTCGAAATTGACTTGAAGCAA
GTATATCGTCATATCCAACGTGCACTTTCTGCATATCAACAAGAAAAAAAAGGTCCAACA
ATTTTATGTGTTCAAGCCCCAATAGCATTAAATTCACTTAATCAACTTATTCCATCACTA
TTTGAATTTCCTCAAACACAAATTCATATAACTGATGATGCTTCATTGTTAGTTGGAATG
GAATGGCAAAAAAATGGCTCAAAATCAATGGTTCGTCATTATCTAAATCACATGCAAGTT
TTCGATTTGATGCTAGAACAATGTCGATATTTTAATATACCTATTGGAAATATGCCTTCT
GATACAGTTCTCTTTGGTGCTGATTTATTTTACGCTCGACATCTTCAAAAACATAATTTC
GTTTTATGGTGGTCATCAACTCATAGACCAGATTTAGGAGGATCAGAAACGGATGATAAC
ACATTGCTTAGTGAATTTGATGAAAATCGAATGGTGAAACAATGCAAGTCGGGTTTTTAT
CCAAACGTTTGTGTAGAACTTGCAATTGACAGTTTAGCTGTTTCAGCATTGCTTCAAAGT
CATCGTATTCAGGAAATGGAAGGAGCTAATGCAGCAATCACATTTGATAATATTCCACAA
GCAAATTTAAATGACATGATAACAAATCCAAATTTACTTCAAATGTTACCCAGTTATGAT
GAAACTGCTTTATGTTCAGCACCCTTCAGAATTATGAGATCAATGGTTAATGGATGGTTG
CGTGAAGTTACAATCAATAGAAATGTTTACAGTGATTTTCAAATTGTTCACTTTTATCGA
TGGATTCGATCTGTAAATTCTTTACTTTATGATCCAGCATTACGACGCTCTCTCAATACG
CTCATGAAGAAACTATTCTTACAAATAATAGCTGAATTTAAAATTCTCGGTGTGGATATT
ATTTATGCCGATTTTACAAAGATTATCATTCACAGTGGCAAAAAGAGTGTGGTTGATGGA
ATAAGTTATGCTGATTATGTTTGTCAAAGTATAAGAAACAAAGAACTATTTCATTCAGTT
CATTTATCATATCAAAAATGTTGGAATTTTCTATTATGGATGGATGATTACAATTTTTCT
GGATTGAGGGGAAAAGTGCCACGAGAATTAGTTGGTGAGAGTGAACAAATTGATGCAGAT
GATGAAGAACTTGCACTTGAAATGAATTGGAATATTTGTGAAGATTTACCTGAAGAAGGA
AAGTGTCGCGATAAATTGGAAAATTTTCTTACTTTGTTCATTGAACAACTCGCTGATGGC
ATTGAATCTTCAAAAGCATTGAAAACTTTATCTCATCATGCATACGATATTGTAACGAAA
TTATATCAGAATTTTGGAAAGAATCAAGAAGGACCAGCAACAGAATTCATCAAAGTGCTT
TGTAAAATTCTTGAAATTGATACAACAGTGACTGATGAACTTGATTCATTAAGAAAGAAC
ATGTTAAGACTTGTTGGATTAGGAGAATTTTCAGACAAAGCCGTTTGGAAAGAGAAAGGA
AAATCTTACATTTTAACTGAAATGATTTGTCAAGCTTGTAATCACTGTCGAGATGTTGAT
TTGATGAAGGATAAGCATCGTGCTATGAAAAATGGTTTACCTGTATGGTTGTGTGCTCAA
TGCTTTGTTAATTATGACACAGAAGATGTTGAACAACGTTTAATTGATGCATTGAATCGT
AAACTCATGTCTTATACTCTTCAAGATCTTCAATGTACTCGCTGTAAAGAAATCAAACAA
GATAACATCATGCAATATTGTCATTGTGCAGGAAATTACACAAATCTTATACAATCAAGT
GAAATTGAAAGTTTAATAACTACTTTTAATCTTGTTGCTGATAATTATTCGATGATTTTA
CTAAAAGAATATACTGATACGCTTCTAAATAATATTTAA

>g14177.t1 Gene=g14177 Length=2192
MYNKYKDNAEKQSQFGLLENNSDDFMSTKAAEQSYKNSRENDYIDSKYGFDRLKDGIERT
GYLINMHSTDILDHEKRLVSALDLYFITMNGSRFKVSVIYQPYFFVIIEQQQIYEVTTFL
QRKYGGQASKIEIVEKEDLDMPNHLTGKKHRMIKLSFHNTTVMNKVRIEINRSVKKNKER
EKSNTFYMQMLSMSLTGRTSNEQIYDYMDFIMDIREHDVPYHVRVSIDLKVFCGLWYNIK
DRGANELPSIVQRPDILERPEPIVLAYDIETTKLPLKFPDAQTDQIMMISYMIDGQGYLI
TNREIVSSDVDDFEYTPKPEFEGNFIVFNEPNELSLIQRFFDHILEVRPHIIVTYNGDFF
DWPFVETRAATYDIDMKREIGYSKNREGNYLSRPSMHMDCLCWVKRDSYLPVGSQGLKAV
AKAKLRYDPVELDPEEMCKKAVEQPQELASYSVSDAVATYYLYMKYVQPFIFALTTIIPM
EPDEVLRKGSGTLCESLLMKEAYHANIIFPNKEQAELNKLTEDGHMLDTETYVGGHIEAL
ESGVFRADLPYRFRLDCGMLQELKNKVSHVLKHAIEVEENIPLSEVTNFDEVTKQIQDVL
QALHDNPNRVEKPVIYHLDVGAMYPNIILTNRLQPSAMVTEQDCAACDFNRPDAACKRQM
DWLWRGEILPATRSEFQRIQQQLETEKFPPLVPGGPYRAFHELSREDRAAIEKKRLSDYC
RKAYKKTKITKLETRTSTICQMENSFYVDTVRAFRDRRYEYKGLTKVAKSEVAKALKSGD
ASEIKAAKGREVLYDSLQLAHKCILNSFYGYVMRKGARWHSMQMGGIVCLTGSNIITKAR
EVIEKVGRPLELDTDGIWCILPGTFPQDFEVFTNLPKKSKITVSYPNAVLNTMVKDHFTN
DQYHNLDKSAENGEVPEYSIRSENSIFFEVDGPYLAMVLPAAKEEGKKLKKRYAVFNFDG
SLAELKGFEIKRRGELQLIKIFQSQVFEAFLQGNTLEKCYQCVAKVANYWLDVLYSKGAN
MPDSELFELISENRSMSKKLEEYGEQKSTSISTAKRLAEFLGDQMVKDAGLACKYIISRK
PEGAPVTERAIPLAIFQSESSVRRFHIRKWLKDSNIDGDVDIRDILDWNYYIERIGGAIQ
KIITIPAALQGVSNPVPRVQHPDWLHKKVLEKNDTFKQRRINELFKATPKPIAEVRDIED
SVGNSQKSQGIPVVTSRKRTRTEENFETQPKTWREALGNPPEIGTTREEFVKWLKFQKKK
WRFQLDQRKKLRGDSGNKRVRQDEVPLVDAVQRGPISTLGGFLKRTQRNLIELTWQIIQI
VPLDLDGHFYLWAIIGDELQKIKLDIPRIFYVNQRTPAPSCENENDKISWKKVHRVLPRS
RPIFNLYQYKVPEQVFRDNGLGMLVDLAAPDIEGIYETQMSLEFRAIMQLGCSCAVQRAE
AKKIASSVNLQRDIFTLDQLEQRMQLHQPYLKEGGNMKKLFLYYHTIPSGKKSMWGLFLT
PLNKAVIIVHDTVRTNQMPSLRNLYTTERQALLSRDDSISDKLPPSEIQFDIHVEIDLKQ
VYRHIQRALSAYQQEKKGPTILCVQAPIALNSLNQLIPSLFEFPQTQIHITDDASLLVGM
EWQKNGSKSMVRHYLNHMQVFDLMLEQCRYFNIPIGNMPSDTVLFGADLFYARHLQKHNF
VLWWSSTHRPDLGGSETDDNTLLSEFDENRMVKQCKSGFYPNVCVELAIDSLAVSALLQS
HRIQEMEGANAAITFDNIPQANLNDMITNPNLLQMLPSYDETALCSAPFRIMRSMVNGWL
REVTINRNVYSDFQIVHFYRWIRSVNSLLYDPALRRSLNTLMKKLFLQIIAEFKILGVDI
IYADFTKIIIHSGKKSVVDGISYADYVCQSIRNKELFHSVHLSYQKCWNFLLWMDDYNFS
GLRGKVPRELVGESEQIDADDEELALEMNWNICEDLPEEGKCRDKLENFLTLFIEQLADG
IESSKALKTLSHHAYDIVTKLYQNFGKNQEGPATEFIKVLCKILEIDTTVTDELDSLRKN
MLRLVGLGEFSDKAVWKEKGKSYILTEMICQACNHCRDVDLMKDKHRAMKNGLPVWLCAQ
CFVNYDTEDVEQRLIDALNRKLMSYTLQDLQCTRCKEIKQDNIMQYCHCAGNYTNLIQSS
EIESLITTFNLVADNYSMILLKEYTDTLLNNI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g14177.t1 CDD cd05779 DNA_polB_epsilon_exo 261 464 5.48339E-143
11 g14177.t1 CDD cd05535 POLBc_epsilon 524 1151 0.0
9 g14177.t1 Coils Coil Coil 560 580 -
8 g14177.t1 Gene3D G3DSA:3.30.420.10 - 264 462 2.8E-58
7 g14177.t1 Gene3D G3DSA:1.10.132.60 - 949 1074 3.7E-9
14 g14177.t1 MobiDBLite mobidb-lite consensus disorder prediction 1200 1229 -
15 g14177.t1 MobiDBLite mobidb-lite consensus disorder prediction 1202 1216 -
4 g14177.t1 PANTHER PTHR10670 DNA POLYMERASE EPSILON CATALYTIC SUBUNIT A 45 2189 0.0
1 g14177.t1 Pfam PF03104 DNA polymerase family B, exonuclease domain 90 420 6.3E-69
2 g14177.t1 Pfam PF00136 DNA polymerase family B 611 1143 2.6E-12
3 g14177.t1 Pfam PF08490 Domain of unknown function (DUF1744) 1522 1921 1.0E-137
12 g14177.t1 SMART SM00486 polmehr3 260 863 3.2E-83
13 g14177.t1 SMART SM01159 DUF1744_2 1520 1922 1.1E-206
6 g14177.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 79 487 2.59E-75
5 g14177.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 489 1176 2.22E-82

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:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0006281 DNA repair BP
GO:0006260 DNA replication BP
GO:0008622 epsilon DNA polymerase complex CC
GO:0003676 nucleic acid binding MF
GO:0003887 DNA-directed DNA polymerase activity MF
GO:0000166 nucleotide binding MF
GO:0008270 zinc ion binding MF

KEGG

Orthology

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.

Raw TPM values