Gene loci information

Transcript annotation

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

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 g12259 g12259.t16 isoform g12259.t16 22050662 22052638
chr_1 g12259 g12259.t16 exon g12259.t16.exon1 22050662 22051972
chr_1 g12259 g12259.t16 cds g12259.t16.CDS1 22050681 22051972
chr_1 g12259 g12259.t16 exon g12259.t16.exon2 22052029 22052638
chr_1 g12259 g12259.t16 cds g12259.t16.CDS2 22052029 22052638
chr_1 g12259 g12259.t16 TTS g12259.t16 22052697 22052697
chr_1 g12259 g12259.t16 TSS g12259.t16 NA NA

Sequences

>g12259.t16 Gene=g12259 Length=1921
CTATAGTTATTTATCAACAATGTGGAATCAACCTTTAAAGATGTGGATTGTTTTAGAATA
TTATATGACACGAGCAAAAACTCTTCTAGAAATTTTAAATCAACTTGATCTCGTTGGAAG
AACATGTGAGTTGGCAAAATTATTTGGGATTCAATTTTTCGAAGTATTATCACGTGGTTC
TCAATTCAGAGTAGAAAGTATGATGTTAAGAATTGCAAAAAGAAGAAATTATGTAGCGGT
TTCGCCAAGTGTTCAACAAAGAACTCATCAACGTGCACCAGAATACATTCCATTAGTTTT
AGAACCACAATCACGATTTTACACTGATTCTGTTATTGTTTTAGATTTTCAAAGTTTATA
TCCAAGCATGATTATTGCTTATAACTATTGTTTTTCAACATGTCTTGGGAGAGTTGAACA
CTTGATGAAAGGTTCACAACAACCTTTTGAATTTGGTGCATATCAATTGAAAGTGTCACC
TGAAAAATTAAGATATCTTCTAGATAATGATTTAGTAACAATTTCACCCTGCGGAGTTGT
TTTTGTAAAATCGTCAGTTAGAGAAGGTGTCTTACCTCGAATGTTGAAAGAAATCCTTGA
TACTCGATTGATGGTCAAACAATCAATGAAACTGTATAAAAATAATAGTGCACTTCAAAG
AATTTTACATTCAAGACAATTAGGATTGAAACTTATTGCTAATGTTACATACGGTTATAC
TGCTGCAAATTTTAGTGGAAGAATGCCATGCATTGAAGTTGGTGATTCTGTTGTGAGCAA
AGGGAGAGAGACACTTGAGAGAGCAATAAATATTGTAGAACAAAATGAGAAATGGGGATG
TAAAGTATGCTATGGCGATACTGATTCGATGTTTGTTCTAGTTCCACATAGAACTAGGGA
AGAAGCTTTTAAAATAGGAGAAGAAATTGCTGAAGTAATTACAAATGATAATCCATACCC
AGTTAAACTGAAACTTGAGAAAGTGTATCAACCATGCATTTTACAGACTAAAAAACGATA
TGTTGGGAACATGTATGAAAGTGCAGATCAAAAAGAACCTATATTTGAGGCTAAAGGAAT
TGAAACTGTTCGTAGAGATGGATGTCCTGCATCGGCAAAAATTTTAGAAAAATCTTTAAA
AATTCTTTTTGATACTTATGATATGAGCAAAGTTAAAGAATATGTATGTCGACAGTTTAC
AAAAATACTCGAAGGAAAATACAGCATTCAAGATTTAATAATTGCAAAGGAATTTCGTGG
AGTTGCTGGATATAAAGAAAAAGCTACAGTTCCTGCTTTAACTTTAACTAAGAAATTTAA
AGTAACAGATCCTCGAAATGAACCACGAAGAGGCGAACGTGTTCCTTTTGTCATTGTTAA
TGGACCACCTAACACAACTTTAATTCGTTTAGTAAAAACTCCGTTGGAAGTACTCAATGA
TGAAAATTTAAAAATCAATAGTCTTTACTATATAACGAAATCAATTATTCCACCACTCAA
TCGATGTCTTTTATTAATTGGTGCAAATGCTCATGATTGGTTCTCTGAACTTCCAAAAAA
ATATCAAGCATTATCGATTGTAAATAATCAAACGAATGATTATCAAACAACACGAAAAGG
AACAATTTCACAATTTTTCAACACAACTAATTGTGCGGTTTGTGAGACTCCATGTGAAAA
TAATTTATGCAATGTGTGTCAAAAAAATTCTCAAGCAGCTGCTCTTGTATTGACGGATAA
AATTTTTAGAATAGAAAGGAAATATATGGGTGTAAAGGAAATGTGTAAAGCGTGTTGTTG
CAGGAATATAAATTTCAAATGCATCTCACTTGACTGTCCTACATTATTTTCTCTAACTCA
AATCAATCGTGATTATGAGCAAGTAGTTCACCTTCGAAGAATATTAAGTGAAATGTTTTA
A

>g12259.t16 Gene=g12259 Length=633
MWNQPLKMWIVLEYYMTRAKTLLEILNQLDLVGRTCELAKLFGIQFFEVLSRGSQFRVES
MMLRIAKRRNYVAVSPSVQQRTHQRAPEYIPLVLEPQSRFYTDSVIVLDFQSLYPSMIIA
YNYCFSTCLGRVEHLMKGSQQPFEFGAYQLKVSPEKLRYLLDNDLVTISPCGVVFVKSSV
REGVLPRMLKEILDTRLMVKQSMKLYKNNSALQRILHSRQLGLKLIANVTYGYTAANFSG
RMPCIEVGDSVVSKGRETLERAINIVEQNEKWGCKVCYGDTDSMFVLVPHRTREEAFKIG
EEIAEVITNDNPYPVKLKLEKVYQPCILQTKKRYVGNMYESADQKEPIFEAKGIETVRRD
GCPASAKILEKSLKILFDTYDMSKVKEYVCRQFTKILEGKYSIQDLIIAKEFRGVAGYKE
KATVPALTLTKKFKVTDPRNEPRRGERVPFVIVNGPPNTTLIRLVKTPLEVLNDENLKIN
SLYYITKSIIPPLNRCLLLIGANAHDWFSELPKKYQALSIVNNQTNDYQTTRKGTISQFF
NTTNCAVCETPCENNLCNVCQKNSQAAALVLTDKIFRIERKYMGVKEMCKACCCRNINFK
CISLDCPTLFSLTQINRDYEQVVHLRRILSEMF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g12259.t16 CDD cd05534 POLBc_zeta 53 503 0.0
11 g12259.t16 Gene3D G3DSA:3.30.420.10 - 1 89 3.3E-5
10 g12259.t16 Gene3D G3DSA:3.90.1600.10 Palm domain of DNA polymerase 93 334 1.8E-90
12 g12259.t16 Gene3D G3DSA:1.10.287.690 Helix hairpin bin 178 239 1.8E-90
9 g12259.t16 Gene3D G3DSA:1.10.132.60 - 353 508 3.9E-39
3 g12259.t16 PANTHER PTHR45812 DNA POLYMERASE ZETA CATALYTIC SUBUNIT 7 622 2.1E-291
4 g12259.t16 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 105 118 2.3E-9
5 g12259.t16 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 220 232 2.3E-9
6 g12259.t16 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 276 284 2.3E-9
1 g12259.t16 Pfam PF00136 DNA polymerase family B 46 497 8.4E-101
2 g12259.t16 Pfam PF14260 C4-type zinc-finger of DNA polymerase delta 545 611 3.7E-7
14 g12259.t16 ProSitePatterns PS00116 DNA polymerase family B signature. 278 286 -
15 g12259.t16 SMART SM00486 polmehr3 1 290 1.7E-7
8 g12259.t16 SUPERFAMILY SSF53098 Ribonuclease H-like 1 69 2.38E-9
7 g12259.t16 SUPERFAMILY SSF56672 DNA/RNA polymerases 92 510 1.67E-110

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:0019985 translesion synthesis BP
GO:0003887 DNA-directed DNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0006281 DNA repair BP
GO:0000166 nucleotide binding MF
GO:0016035 zeta DNA polymerase complex CC
GO:0003676 nucleic acid binding MF

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.

Raw TPM values