Gene loci information

Transcript annotation

  • This transcript has been annotated as Poly [ADP-ribose] polymerase.

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_3 g3457 g3457.t1 TTS g3457.t1 25529888 25529888
chr_3 g3457 g3457.t1 isoform g3457.t1 25530109 25533644
chr_3 g3457 g3457.t1 exon g3457.t1.exon1 25530109 25530302
chr_3 g3457 g3457.t1 cds g3457.t1.CDS1 25530109 25530302
chr_3 g3457 g3457.t1 exon g3457.t1.exon2 25530393 25530566
chr_3 g3457 g3457.t1 cds g3457.t1.CDS2 25530393 25530566
chr_3 g3457 g3457.t1 exon g3457.t1.exon3 25530633 25530642
chr_3 g3457 g3457.t1 cds g3457.t1.CDS3 25530633 25530642
chr_3 g3457 g3457.t1 exon g3457.t1.exon4 25530757 25531896
chr_3 g3457 g3457.t1 cds g3457.t1.CDS4 25530757 25531896
chr_3 g3457 g3457.t1 exon g3457.t1.exon5 25531992 25532886
chr_3 g3457 g3457.t1 cds g3457.t1.CDS5 25531992 25532886
chr_3 g3457 g3457.t1 exon g3457.t1.exon6 25532946 25533457
chr_3 g3457 g3457.t1 cds g3457.t1.CDS6 25532946 25533457
chr_3 g3457 g3457.t1 exon g3457.t1.exon7 25533534 25533644
chr_3 g3457 g3457.t1 cds g3457.t1.CDS7 25533534 25533644
chr_3 g3457 g3457.t1 TSS g3457.t1 25533895 25533895

Sequences

>g3457.t1 Gene=g3457 Length=3036
ATGGAAGAATTACCTTATAAAGTTGAATATGCCAAGACAGGTCGAGCAAAGTGTCGTGGG
TGCAAGATAAATATTGAAAAGGACGAATTAAGACTAGCTGCATTGGTTCAGTCTTTTTTT
CACGATGGTAAAGATTGTCATTGGTTTCACTTAAATTGCTTCTTTCAAAAACATCGACCA
AAAGCCATAGATGATATTGATCATTTTGAGGAAATTCGTATTGAGGATCAAGAAAATATT
CGTCAAAAATTGGATGCAACAAAAGGTATTTTACTGCCAGAACCTAAAGGAAAAAAGAAG
GGTAAGAAGCGTGCGGCTGAAGATAGTAAAACAGCTGCATTTAATGCAACGGCACTTAAT
GATTTTGGTGTTGAATATGCTAAATCTGGACGTTCCGCTTGTGCTGGATGCGGTAATAAC
ATAATGGTCAACGAAGTTCGAATTAAAAAAATGGATTACACAACAGAAGTTGGTATGAAA
TTTGGTGGTCAACCTTTTTGGCATCATGTAGATTGTTTTGCAAAAATTCGTGGTGATTAC
AACTTTTATCTTGATGGATCAGACTTGCCTGGATTTTCTGAACTTTCACCAGCTGATAAA
AAAATAGTCAAAAAAGCTATCAAAGCAATTGAAATTACTGAAGCGCAAGCAAAGAAATTG
AAAACTGAACCTCGAGATAAGGATGAAGTAGAAGCTGAGAATGCACTTGAAAAATTGATT
ACAGAACAGACAAAATTATTATTTAAAGTTCGAGATGAAATTCAATTCCTCAAAAAGAGC
GATTTACAAAACATTCTTTTCGTAAATGATTCCGGCATGGTTAGTGGATCTGATGCATTG
ATTGAACGGTGTTCTGACTTTCTTACATTCGGAGCTATCAAAAAATGTAAGAAATGTAAG
AATGGTGATATGATTTTCGCTAAATATGGTTATCGATGTAATGGAAATATTGATGAATGG
ACAATGTGTGAAAATTTTGAGGAGAAGCCTGAACGTGTTAAGTGCAAAATTCCAAAAGAA
CTTAAGGAATCGAAAGGAAACAAAAAATCTGAGAAAAACTTCTTCGCCAAATACAAATCC
TTAGTTAAAGATCGTGCTGTTCGTCCACAAATAAAGAAGGAAATCAAGAAAGATGAAGAA
GATGGAAAACGTATTTATAAAGTTGAACGCGAAAGAGAACCTTTATATGGTATGCACTGT
GTTTTAATTAGCAACAACAAAGGATTAAAGGAAGAATTAAAGACAAAAATTACACGTTTG
GGAGGTAAAGTTGTTACAACATTGCAAGAACATATTGCATTTGTTATCAGTAATAATGAT
GAAGTTGAAAAGATGAACAAGCGAATGCAAGAAGTAAAATCGTTGGATATTCAAGTAGTT
GATGAAAAGTTTATTGATGCCATTGAAAAACTAAAACGTGCTGAAGTGATTGAAAAAATA
AAATCGATGTCGATCTGTGATTGGGGTTCAGATCCTTTGACTAGGATTCCAGCAGAAGAA
GAGAAGAAAACTGAAAGGGAATCAATTTATAATCGTAACAAGAAAAAGACAGCTGTGATG
AAATTGAAAAATGGTACTGCTATTGATCCAGCATCGGGACTTTCGGATGTTGCCCATGTT
TATAAGGACAAATTAACTAACATTTTATATACAACAGTTCTTACTAAAATAGACATTCAG
AAGAACAAGAATTCTTATTACAAATTACAAGTTCTTGAAAGCGATATGGAACGAAATTAC
TGGCTTTTCCGATCATGGGGTAGAATAGGAACGGATGTTGGTGATAATAAAACTGAAAAA
TGTTTTTCAGTTGAAGAAGCCATTACTGAGTTTGAAAGACTTTTTGAAGAAAAAACTGGA
AACATTTTCGGCGCTCCATTCCAAAAGAAGCCCAACAGTTATACGCTTGTTGAAGTCGAT
TACGAAAATGAAGATGAAAAGAACAAAAAGAAGGAAGAACTTGAGAAAATTCCATCGAAG
TTGCCGACATCTGTCCAAGATCTTGTTAAAATGATATTCGATATTGATACTATGAAGAAA
ACCATGCTTGAATTTGAACTTGATTTGGAAAAAATGCCTCTTGGTCGATTATCCAGCAAA
CAATTGCATGAAGCATATACAGTGTTAAATGATCTTGATGAATTGATTAAAAGCGGTGAT
AATAATGAAAGCAAGTTCATTGGTTTCAGCAACAAGTTCTTTTCACTTGTTCCTCATAGT
TTTGGCATGAATAAGGCACCTGTTATCAATACAGTTGAAATGATTAAGCAAAAACGTGAA
ATGATTGATTCCTTGATGGAGATTGAAATTGCTTATGCATTTATTAAGGACGATGAGAAG
AGTAACACTGACGTGAATCCACTTGATGCTCACTATGCTAAATTGAAGACAGATCTAAAA
CCACTTGATAAAAATAATGATGAATTTAAACTTATTGAGTCTTATATTAAAAATACACAC
GCTGAAACTCACAATCAATATACACTTGAAATTGAAGATGTATTTAAAGTTAAGCGTGAA
AATGAGCATCGTCGTTATAAACCATTCAAGAAACTTCACAATCGTCAATTACTCTGGCAC
GGAAGTCGTCTTACAAATTATGTTGGTATTTTGTCACACGGTTTGAAAATTGCACCACCA
GAAGCTCCCTGTACTGGCTATATGTTTGGTAAGGGCGTATACTTTGCTGATATGGTCAGC
AAATCTGCCAACTACTGTTGCACATCACCTCGACAACCAATTGGTCTTATGCTCCTCTCT
GAAGTTGCATTAGGTGATATGTATGAATTGACAAATGCAAAGTACATCAACAAATTACCT
CCTGGCAAACATTCATGTAAAGGTATTGGAAAGACATCACCAAATCCAGAACAGTTTCAA
GTTAGAGAAGACGGAGTTACCATTCCATGCGGTCAGCCAAAAACTAATGATAAATTGCGT
TCAGAATTGCTTTACAACGAGTACATTGTATATGATGTTGCTCAAGTTAATATTCAATAT
CTACTTAAGCTTAAATTCAACTATAAACGCCAATAA

>g3457.t1 Gene=g3457 Length=1011
MEELPYKVEYAKTGRAKCRGCKINIEKDELRLAALVQSFFHDGKDCHWFHLNCFFQKHRP
KAIDDIDHFEEIRIEDQENIRQKLDATKGILLPEPKGKKKGKKRAAEDSKTAAFNATALN
DFGVEYAKSGRSACAGCGNNIMVNEVRIKKMDYTTEVGMKFGGQPFWHHVDCFAKIRGDY
NFYLDGSDLPGFSELSPADKKIVKKAIKAIEITEAQAKKLKTEPRDKDEVEAENALEKLI
TEQTKLLFKVRDEIQFLKKSDLQNILFVNDSGMVSGSDALIERCSDFLTFGAIKKCKKCK
NGDMIFAKYGYRCNGNIDEWTMCENFEEKPERVKCKIPKELKESKGNKKSEKNFFAKYKS
LVKDRAVRPQIKKEIKKDEEDGKRIYKVEREREPLYGMHCVLISNNKGLKEELKTKITRL
GGKVVTTLQEHIAFVISNNDEVEKMNKRMQEVKSLDIQVVDEKFIDAIEKLKRAEVIEKI
KSMSICDWGSDPLTRIPAEEEKKTERESIYNRNKKKTAVMKLKNGTAIDPASGLSDVAHV
YKDKLTNILYTTVLTKIDIQKNKNSYYKLQVLESDMERNYWLFRSWGRIGTDVGDNKTEK
CFSVEEAITEFERLFEEKTGNIFGAPFQKKPNSYTLVEVDYENEDEKNKKKEELEKIPSK
LPTSVQDLVKMIFDIDTMKKTMLEFELDLEKMPLGRLSSKQLHEAYTVLNDLDELIKSGD
NNESKFIGFSNKFFSLVPHSFGMNKAPVINTVEMIKQKREMIDSLMEIEIAYAFIKDDEK
SNTDVNPLDAHYAKLKTDLKPLDKNNDEFKLIESYIKNTHAETHNQYTLEIEDVFKVKRE
NEHRRYKPFKKLHNRQLLWHGSRLTNYVGILSHGLKIAPPEAPCTGYMFGKGVYFADMVS
KSANYCCTSPRQPIGLMLLSEVALGDMYELTNAKYINKLPPGKHSCKGIGKTSPNPEQFQ
VREDGVTIPCGQPKTNDKLRSELLYNEYIVYDVAQVNIQYLLKLKFNYKRQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g3457.t1 CDD cd17747 BRCT_PARP1 395 470 3.10003E-21
28 g3457.t1 CDD cd08001 WGR_PARP1_like 538 641 1.59064E-39
27 g3457.t1 CDD cd01437 parp_like 658 1005 8.04678E-174
24 g3457.t1 Coils Coil Coil 203 223 -
16 g3457.t1 Gene3D G3DSA:3.30.1740.10 - 1 111 8.2E-29
17 g3457.t1 Gene3D G3DSA:3.30.1740.10 - 115 217 5.0E-26
20 g3457.t1 Gene3D G3DSA:1.10.20.130 - 218 291 1.4E-10
23 g3457.t1 Gene3D G3DSA:2.20.25.630 - 292 351 2.2E-15
21 g3457.t1 Gene3D G3DSA:3.40.50.10190 - 387 495 3.4E-25
22 g3457.t1 Gene3D G3DSA:2.20.140.10 q64v53_bacfr domain like 512 656 2.1E-43
18 g3457.t1 Gene3D G3DSA:3.90.228.10 - 661 1005 2.2E-150
19 g3457.t1 Gene3D G3DSA:1.20.142.10 - 674 783 2.2E-150
8 g3457.t1 PANTHER PTHR10459 DNA LIGASE 47 1005 3.8E-246
9 g3457.t1 PANTHER PTHR10459:SF80 POLY [ADP-RIBOSE] POLYMERASE 1 47 1005 3.8E-246
25 g3457.t1 PIRSF PIRSF000489 NAD_ADPRT 1 1010 0.0
2 g3457.t1 Pfam PF00645 Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region 9 83 1.1E-16
1 g3457.t1 Pfam PF00645 Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region 125 207 2.9E-13
7 g3457.t1 Pfam PF08063 PADR1 (NUC008) domain 281 332 2.6E-17
5 g3457.t1 Pfam PF00533 BRCA1 C Terminus (BRCT) domain 394 466 1.2E-5
3 g3457.t1 Pfam PF05406 WGR domain 550 623 4.9E-22
6 g3457.t1 Pfam PF02877 Poly(ADP-ribose) polymerase, regulatory domain 659 792 1.8E-46
4 g3457.t1 Pfam PF00644 Poly(ADP-ribose) polymerase catalytic domain 807 1006 4.4E-76
34 g3457.t1 ProSitePatterns PS00347 Poly(ADP-ribose) polymerase zinc finger domain signature. 18 53 -
38 g3457.t1 ProSiteProfiles PS50064 Poly(ADP-ribose) polymerase zinc finger domain profile. 6 88 29.637
37 g3457.t1 ProSiteProfiles PS50064 Poly(ADP-ribose) polymerase zinc finger domain profile. 122 211 29.818
36 g3457.t1 ProSiteProfiles PS50172 BRCT domain profile. 390 465 11.114
35 g3457.t1 ProSiteProfiles PS51060 PARP alpha-helical domain profile. 658 776 40.137
39 g3457.t1 ProSiteProfiles PS51059 PARP catalytic domain profile. 786 1011 105.713
32 g3457.t1 SMART SM01336 zf_PARP_3 9 85 1.0E-34
31 g3457.t1 SMART SM01336 zf_PARP_3 125 208 1.5E-27
30 g3457.t1 SMART SM01335 PADR1_2 280 334 6.9E-22
33 g3457.t1 SMART SM00292 BRCT_7 392 472 1.7E-5
29 g3457.t1 SMART SM00773 WGR_cls 550 628 5.5E-28
13 g3457.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 2 87 2.52E-26
12 g3457.t1 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 119 219 7.6E-23
14 g3457.t1 SUPERFAMILY SSF52113 BRCT domain 390 471 2.62E-7
11 g3457.t1 SUPERFAMILY SSF142921 WGR domain-like 517 638 4.45E-33
10 g3457.t1 SUPERFAMILY SSF47587 Domain of poly(ADP-ribose) polymerase 659 793 7.59E-42
15 g3457.t1 SUPERFAMILY SSF56399 ADP-ribosylation 795 1009 3.24E-75

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:0008270 zinc ion binding MF
GO:0051287 NAD binding MF
GO:0003950 NAD+ ADP-ribosyltransferase activity MF
GO:0006471 protein ADP-ribosylation BP

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