General information for g12259.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA polymerase zeta catalytic subunit.
Parent gene
- The parent gene g12259 is located on chr_1: 22052638..22053915 (+ 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 | g12259 | g12259.t1 | TSS | g12259.t1 | 22047073 | 22047073 |
| chr_1 | g12259 | g12259.t1 | isoform | g12259.t1 | 22047141 | 22052638 |
| chr_1 | g12259 | g12259.t1 | exon | g12259.t1.exon1 | 22047141 | 22047317 |
| chr_1 | g12259 | g12259.t1 | cds | g12259.t1.CDS1 | 22047141 | 22047317 |
| chr_1 | g12259 | g12259.t1 | exon | g12259.t1.exon2 | 22047378 | 22047455 |
| chr_1 | g12259 | g12259.t1 | cds | g12259.t1.CDS2 | 22047378 | 22047455 |
| chr_1 | g12259 | g12259.t1 | exon | g12259.t1.exon3 | 22047714 | 22051972 |
| chr_1 | g12259 | g12259.t1 | cds | g12259.t1.CDS3 | 22047714 | 22051972 |
| chr_1 | g12259 | g12259.t1 | exon | g12259.t1.exon4 | 22052029 | 22052638 |
| chr_1 | g12259 | g12259.t1 | cds | g12259.t1.CDS4 | 22052029 | 22052638 |
| chr_1 | g12259 | g12259.t1 | TTS | g12259.t1 | 22052697 | 22052697 |
Sequences
>g12259.t1 Gene=g12259 Length=5124
ATGGATAACGTGTTATCTATTAAAATTATTACTTGTGATTATTATAATACTGCACCAATA
CAAAATCTTGATGTGACATATTCAGAATTTCGTAAAATTGATGTGAAAAATGTGCCGGTA
TTAAGAATTTTCGGTATAACAAAAGAAAAATTGAAAATTTGTTGCAATATTCATAATGTT
TTTCCATATCTTTTTGTTCCATGTCCTGAAGCAGATTTAGAGAAAATCGATCCTCTTATG
AAAGAAATGGCTCAACAAATTGATCTAAAAATCAACTCATCTTTCGGTCAATCTAACAGT
GCTCAACAACATGTTTATCGAATATCTCTCTGCAAAGGAACGTTTTTTTATGGCTATCAT
CACAATCAGAGTCAGTTGTTTAAAATTGAACTGTATAATCCAAATCTGCTTAAAAGAACT
GCTGGACTCTTACAAAATGGGTTGATAATGGGGAGAATTTTTCAAAGTTATGAAACTCAC
ATTCCATATGTTATGAGATTTTTCATAGACTTTAATTTATTTGGGATGAGTTATCTTCAT
GTGCCAATGAATAAAGTGCATACACGTCACACAACAAGTGAAGGAAGATACAAAAAAAGA
TCAGTGTCACATCTTGAAGTGGATTTTAGTGCAGCACATATTATTAATCGTATAGCTTTA
TATGAGAGTGAAGAGACTGATAAAGCAGCTAATATTGGGATACAATTTCTATGGGAGGAT
GAGAAAAGAAGAAGAGAACTTGAATTTAATTCACAAGACATGCCAGAATTAAAACCAGCT
GAGAGTGAATTGAGACCATTTTATCAAATTGCTTCGAGTGAAACTTTTTACAAAAATGCA
CTCCTTAATAAAATCAATTCACTCTTTGCAAAAACTGAAAATTCAGATGAGGCTGAAACA
TCATCAACAAGTGCAACAAAGATTAAGAAGAAATTCAATTTACAACAATTTCTTGAATGT
TCAACATATGGTGTCGATTTTTCTCAAAGTTTTTCAGAAGATTTAAATTCTAGTATAGTA
TCAAATGAAAGCCCACCATTAGAGGATCTTGAGAAAGAATATCTTCAATTAGATAAAATT
GAAGAAAAGCAAGAAATTGAAGAAATTCTTAATAATTTGGAAAATGTATGTAACAGTGAT
GAAGAAAATGATAGTATTCTTGCACCTTTAACTCAAACAATTTCAAAAAATAGTCAAATA
AAAGAAAATGAAAATCAATTAAACTATTCAATAAATGAAATAACTAAAAATGATGATGAG
GAAGATGTAGAAGATGAAGACACATTTAATATGACACTAGCTGATATGGAGGCAGCTCTT
TATAACTTGAGTGATAAAATTGATATTCCACAATTAGATGGTGCAATCGATGACATCAAT
TCGAAAAACACTCCGTCAACCTCTTCATCTGTTTTATCATTCCAAGATATTCAAAATAAT
TTACAATCTTTGGCTGCTCATTTTATGTCTAATGAAGATGTTGAAATGAAAGAAACCGAT
GATGTAAATGAAACTAATTTTGATGAAACTAATGATGAGATGATGAAAAGTTTTTATAAT
GAATCGCAATTTTATGATTTTAATGATTCTGATTCAAGTCATCCTGATGAAGTCATTGTA
AAACAAGAATGTATAACTCAAGAAAGTACAAGTAGCAAAACTTGCATAATTACACCTAAC
ATTGAACCACCAGATCCGAAAAAAGTTGAAGAAACATTCTTTAAATATGACATTACTGAA
ACAACTAATAAGAGTGCTTTTTATAGCAATCCAAAAGATGTTACTGGTAAAAAGGAAATT
GGAAACAAAATCCTTGAAATTAAAGGCAATCGTGTGAGTCATTGTGAAGATTTCAAAAGT
GTTCTATTTGATTCAAGTGAATTTAAAAAATATCAAAAGAAAAAAATCATGTTTAATTTA
GGATATATGCCAAAGAACAGTAAATCAATTTATGAAATGATAAATAATAAATCAGAAGTA
AAAATTCACCCAATCATTGAACCACCCACTTATGAAGACGCAAAAAATTGGTTGAAATCC
ACAATTAAAACAAAAGAGCAACCTCTACGACCAACAAACATTGAAGAAGATAGTCCAATA
AAAGTTAAACGAGAGAAAACTATAAATGTTATGAAAAAAGAAGATAACGATGATGAAAAT
ATTGAAGAGTCACAAGATCTTGATAAAACTTTGATTCCAGAAACACCCAATACGTGTGAT
TTTCTCAACATGACTGTGATACAAAATTCAAATGAAATTGACACATCTTCACTGCAAGAT
TACGTTGAAGATGGCATTTATCTAAGTTATAGTGCAAGAAGAAAGAGAAAAAGGAAAATG
AAGCAAAGTTTTAGCAAACGGTTTCAAGAGATAATGAAAGCAAAATTGACTTCTGGTAAA
ACCAAAGATGAAAATATTGCAAATTCTCCTAATTCATCGTTCACAGAAACCTCAGATTCT
TCTGATGATTTCTTAAAAACAATCGATCCGAAACCTTCAGAAAACACACCTAATTCATTT
TTTATTCCTGATGCAAATATTTCACTTGATGAAAGCAGTTATGAATCATCAATGATGAAT
AATTCATTTGGGTTTAAAGTTAAATTAGAAAGTCTTCATACTAATGATGAACATATTGAT
CTCACAATTCTTTCTATGGAATTACATTGCGTCACAAAAGGAGAATTCAAACCGAATCCT
GAAACTGATGAAATTTCTGCAATTTTTTGGTCTGTTGAAGGATATTATATTAATGGTCAA
TCAACAACTCAGAGTGGGATAATTGTAGTATTTGAAGAAAATTTAGGATTTTTCAAATCA
AATATTGAAATTTTAAAAGTAAAAAATGAAATGGAGTTACTTGATCAATTTTTTCAAAAA
ATTCGTGCATTTGATCCTGATATTTTTGCTGGATATGAAATAGAATTAAATTCTTGGGGA
TATTTAATTGAACGTGGTTTAGTTCTTAATATGAATTTATGTAATGCTCTCTCACGAATG
CCTCTTGAAAAAGAATACAAGACAAAAATTATTCAAGAAAATGATCATGATCATGATCAA
GGTGACTATCAAACAGAACAGAGAATCCCAGGGAGAATTTTATTGGACGTTTGGCGTTTA
ATGCGACATGAAATTGCACTTACTTCTTACACTTTTGAAAATATTTCATATCATATTCTT
CATCGAAGATATCCTAAACATTCCTATAGTTATTTATCAACAATGTGGAATCAACCTTTA
AAGATGTGGATTGTTTTAGAATATTATATGACACGAGCAAAAACTCTTCTAGAAATTTTA
AATCAACTTGATCTCGTTGGAAGAACATGTGAGTTGGCAAAATTATTTGGGATTCAATTT
TTCGAAGTATTATCACGTGGTTCTCAATTCAGAGTAGAAAGTATGATGTTAAGAATTGCA
AAAAGAAGAAATTATGTAGCGGTTTCGCCAAGTGTTCAACAAAGAACTCATCAACGTGCA
CCAGAATACATTCCATTAGTTTTAGAACCACAATCACGATTTTACACTGATTCTGTTATT
GTTTTAGATTTTCAAAGTTTATATCCAAGCATGATTATTGCTTATAACTATTGTTTTTCA
ACATGTCTTGGGAGAGTTGAACACTTGATGAAAGGTTCACAACAACCTTTTGAATTTGGT
GCATATCAATTGAAAGTGTCACCTGAAAAATTAAGATATCTTCTAGATAATGATTTAGTA
ACAATTTCACCCTGCGGAGTTGTTTTTGTAAAATCGTCAGTTAGAGAAGGTGTCTTACCT
CGAATGTTGAAAGAAATCCTTGATACTCGATTGATGGTCAAACAATCAATGAAACTGTAT
AAAAATAATAGTGCACTTCAAAGAATTTTACATTCAAGACAATTAGGATTGAAACTTATT
GCTAATGTTACATACGGTTATACTGCTGCAAATTTTAGTGGAAGAATGCCATGCATTGAA
GTTGGTGATTCTGTTGTGAGCAAAGGGAGAGAGACACTTGAGAGAGCAATAAATATTGTA
GAACAAAATGAGAAATGGGGATGTAAAGTATGCTATGGCGATACTGATTCGATGTTTGTT
CTAGTTCCACATAGAACTAGGGAAGAAGCTTTTAAAATAGGAGAAGAAATTGCTGAAGTA
ATTACAAATGATAATCCATACCCAGTTAAACTGAAACTTGAGAAAGTGTATCAACCATGC
ATTTTACAGACTAAAAAACGATATGTTGGGAACATGTATGAAAGTGCAGATCAAAAAGAA
CCTATATTTGAGGCTAAAGGAATTGAAACTGTTCGTAGAGATGGATGTCCTGCATCGGCA
AAAATTTTAGAAAAATCTTTAAAAATTCTTTTTGATACTTATGATATGAGCAAAGTTAAA
GAATATGTATGTCGACAGTTTACAAAAATACTCGAAGGAAAATACAGCATTCAAGATTTA
ATAATTGCAAAGGAATTTCGTGGAGTTGCTGGATATAAAGAAAAAGCTACAGTTCCTGCT
TTAACTTTAACTAAGAAATTTAAAGTAACAGATCCTCGAAATGAACCACGAAGAGGCGAA
CGTGTTCCTTTTGTCATTGTTAATGGACCACCTAACACAACTTTAATTCGTTTAGTAAAA
ACTCCGTTGGAAGTACTCAATGATGAAAATTTAAAAATCAATAGTCTTTACTATATAACG
AAATCAATTATTCCACCACTCAATCGATGTCTTTTATTAATTGGTGCAAATGCTCATGAT
TGGTTCTCTGAACTTCCAAAAAAATATCAAGCATTATCGATTGTAAATAATCAAACGAAT
GATTATCAAACAACACGAAAAGGAACAATTTCACAATTTTTCAACACAACTAATTGTGCG
GTTTGTGAGACTCCATGTGAAAATAATTTATGCAATGTGTGTCAAAAAAATTCTCAAGCA
GCTGCTCTTGTATTGACGGATAAAATTTTTAGAATAGAAAGGAAATATATGGGTGTAAAG
GAAATGTGTAAAGCGTGTTGTTGCAGGAATATAAATTTCAAATGCATCTCACTTGACTGT
CCTACATTATTTTCTCTAACTCAAATCAATCGTGATTATGAGCAAGTAGTTCACCTTCGA
AGAATATTAAGTGAAATGTTTTAA
>g12259.t1 Gene=g12259 Length=1707
MDNVLSIKIITCDYYNTAPIQNLDVTYSEFRKIDVKNVPVLRIFGITKEKLKICCNIHNV
FPYLFVPCPEADLEKIDPLMKEMAQQIDLKINSSFGQSNSAQQHVYRISLCKGTFFYGYH
HNQSQLFKIELYNPNLLKRTAGLLQNGLIMGRIFQSYETHIPYVMRFFIDFNLFGMSYLH
VPMNKVHTRHTTSEGRYKKRSVSHLEVDFSAAHIINRIALYESEETDKAANIGIQFLWED
EKRRRELEFNSQDMPELKPAESELRPFYQIASSETFYKNALLNKINSLFAKTENSDEAET
SSTSATKIKKKFNLQQFLECSTYGVDFSQSFSEDLNSSIVSNESPPLEDLEKEYLQLDKI
EEKQEIEEILNNLENVCNSDEENDSILAPLTQTISKNSQIKENENQLNYSINEITKNDDE
EDVEDEDTFNMTLADMEAALYNLSDKIDIPQLDGAIDDINSKNTPSTSSSVLSFQDIQNN
LQSLAAHFMSNEDVEMKETDDVNETNFDETNDEMMKSFYNESQFYDFNDSDSSHPDEVIV
KQECITQESTSSKTCIITPNIEPPDPKKVEETFFKYDITETTNKSAFYSNPKDVTGKKEI
GNKILEIKGNRVSHCEDFKSVLFDSSEFKKYQKKKIMFNLGYMPKNSKSIYEMINNKSEV
KIHPIIEPPTYEDAKNWLKSTIKTKEQPLRPTNIEEDSPIKVKREKTINVMKKEDNDDEN
IEESQDLDKTLIPETPNTCDFLNMTVIQNSNEIDTSSLQDYVEDGIYLSYSARRKRKRKM
KQSFSKRFQEIMKAKLTSGKTKDENIANSPNSSFTETSDSSDDFLKTIDPKPSENTPNSF
FIPDANISLDESSYESSMMNNSFGFKVKLESLHTNDEHIDLTILSMELHCVTKGEFKPNP
ETDEISAIFWSVEGYYINGQSTTQSGIIVVFEENLGFFKSNIEILKVKNEMELLDQFFQK
IRAFDPDIFAGYEIELNSWGYLIERGLVLNMNLCNALSRMPLEKEYKTKIIQENDHDHDQ
GDYQTEQRIPGRILLDVWRLMRHEIALTSYTFENISYHILHRRYPKHSYSYLSTMWNQPL
KMWIVLEYYMTRAKTLLEILNQLDLVGRTCELAKLFGIQFFEVLSRGSQFRVESMMLRIA
KRRNYVAVSPSVQQRTHQRAPEYIPLVLEPQSRFYTDSVIVLDFQSLYPSMIIAYNYCFS
TCLGRVEHLMKGSQQPFEFGAYQLKVSPEKLRYLLDNDLVTISPCGVVFVKSSVREGVLP
RMLKEILDTRLMVKQSMKLYKNNSALQRILHSRQLGLKLIANVTYGYTAANFSGRMPCIE
VGDSVVSKGRETLERAINIVEQNEKWGCKVCYGDTDSMFVLVPHRTREEAFKIGEEIAEV
ITNDNPYPVKLKLEKVYQPCILQTKKRYVGNMYESADQKEPIFEAKGIETVRRDGCPASA
KILEKSLKILFDTYDMSKVKEYVCRQFTKILEGKYSIQDLIIAKEFRGVAGYKEKATVPA
LTLTKKFKVTDPRNEPRRGERVPFVIVNGPPNTTLIRLVKTPLEVLNDENLKINSLYYIT
KSIIPPLNRCLLLIGANAHDWFSELPKKYQALSIVNNQTNDYQTTRKGTISQFFNTTNCA
VCETPCENNLCNVCQKNSQAAALVLTDKIFRIERKYMGVKEMCKACCCRNINFKCISLDC
PTLFSLTQINRDYEQVVHLRRILSEMF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g12259.t1 | CDD | cd05778 | DNA_polB_zeta_exo | 878 | 1101 | 3.58407E-66 |
| 16 | g12259.t1 | CDD | cd05534 | POLBc_zeta | 1127 | 1577 | 0.0 |
| 15 | g12259.t1 | Coils | Coil | Coil | 347 | 383 | - |
| 13 | g12259.t1 | Gene3D | G3DSA:3.30.342.10 | DNA Polymerase | 22 | 194 | 9.4E-33 |
| 12 | g12259.t1 | Gene3D | G3DSA:3.30.420.10 | - | 881 | 1103 | 5.4E-38 |
| 11 | g12259.t1 | Gene3D | G3DSA:3.90.1600.10 | Palm domain of DNA polymerase | 1167 | 1408 | 1.0E-89 |
| 14 | g12259.t1 | Gene3D | G3DSA:1.10.287.690 | Helix hairpin bin | 1252 | 1313 | 1.0E-89 |
| 10 | g12259.t1 | Gene3D | G3DSA:1.10.132.60 | - | 1427 | 1582 | 1.7E-38 |
| 20 | g12259.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 798 | 821 | - |
| 21 | g12259.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 801 | 821 | - |
| 4 | g12259.t1 | PANTHER | PTHR45812 | DNA POLYMERASE ZETA CATALYTIC SUBUNIT | 3 | 1696 | 0.0 |
| 6 | g12259.t1 | PRINTS | PR00106 | DNA-directed DNA-polymerase family B signature | 1179 | 1192 | 3.8E-8 |
| 5 | g12259.t1 | PRINTS | PR00106 | DNA-directed DNA-polymerase family B signature | 1294 | 1306 | 3.8E-8 |
| 7 | g12259.t1 | PRINTS | PR00106 | DNA-directed DNA-polymerase family B signature | 1350 | 1358 | 3.8E-8 |
| 2 | g12259.t1 | Pfam | PF03104 | DNA polymerase family B, exonuclease domain | 47 | 192 | 2.9E-15 |
| 1 | g12259.t1 | Pfam | PF03104 | DNA polymerase family B, exonuclease domain | 875 | 1054 | 6.9E-16 |
| 3 | g12259.t1 | Pfam | PF00136 | DNA polymerase family B | 1120 | 1571 | 8.9E-100 |
| 19 | g12259.t1 | ProSitePatterns | PS00116 | DNA polymerase family B signature. | 1352 | 1360 | - |
| 18 | g12259.t1 | SMART | SM00486 | polmehr3 | 879 | 1364 | 3.4E-96 |
| 9 | g12259.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 30 | 1126 | 5.73E-70 |
| 8 | g12259.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 1166 | 1584 | 1.56E-109 |
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 transcript has been annotated with K02350 (DNA polymerase zeta)
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.
