General information for g3457.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Poly [ADP-ribose] polymerase.
Parent gene
- The parent gene g3457 is located on chr_3: 25532361..25533893 (- 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_3 | g3457 | g3457.t2 | isoform | g3457.t2 | 25532361 | 25533893 |
| chr_3 | g3457 | g3457.t2 | exon | g3457.t2.exon1 | 25532361 | 25532886 |
| chr_3 | g3457 | g3457.t2 | cds | g3457.t2.CDS1 | 25532361 | 25532886 |
| chr_3 | g3457 | g3457.t2 | exon | g3457.t2.exon2 | 25532946 | 25533457 |
| chr_3 | g3457 | g3457.t2 | cds | g3457.t2.CDS2 | 25532946 | 25533457 |
| chr_3 | g3457 | g3457.t2 | exon | g3457.t2.exon3 | 25533534 | 25533673 |
| chr_3 | g3457 | g3457.t2 | cds | g3457.t2.CDS3 | 25533534 | 25533644 |
| chr_3 | g3457 | g3457.t2 | exon | g3457.t2.exon4 | 25533793 | 25533893 |
| chr_3 | g3457 | g3457.t2 | TSS | g3457.t2 | 25533895 | 25533895 |
| chr_3 | g3457 | g3457.t2 | TTS | g3457.t2 | NA | NA |
Sequences
>g3457.t2 Gene=g3457 Length=1279
ATTTGGCGCCATTCTTTTGTTTTGTTAACTCGCGTTATTGAAAATTTTTTAAAGATATCT
TATTAAAACTAATTTACACTATTTTTCTACTTGTTTATATGTAAGATTTGCGATTTATCA
TAAAATTACAATGGAAGAATTACCTTATAAAGTTGAATATGCCAAGACAGGTCGAGCAAA
GTGTCGTGGGTGCAAGATAAATATTGAAAAGGACGAATTAAGACTAGCTGCATTGGTTCA
GTCTTTTTTTCACGATGGTAAAGATTGTCATTGGTTTCACTTAAATTGCTTCTTTCAAAA
ACATCGACCAAAAGCCATAGATGATATTGATCATTTTGAGGAAATTCGTATTGAGGATCA
AGAAAATATTCGTCAAAAATTGGATGCAACAAAAGGTATTTTACTGCCAGAACCTAAAGG
AAAAAAGAAGGGTAAGAAGCGTGCGGCTGAAGATAGTAAAACAGCTGCATTTAATGCAAC
GGCACTTAATGATTTTGGTGTTGAATATGCTAAATCTGGACGTTCCGCTTGTGCTGGATG
CGGTAATAACATAATGGTCAACGAAGTTCGAATTAAAAAAATGGATTACACAACAGAAGT
TGGTATGAAATTTGGTGGTCAACCTTTTTGGCATCATGTAGATTGTTTTGCAAAAATTCG
TGGTGATTACAACTTTTATCTTGATGGATCAGACTTGCCTGGATTTTCTGAACTTTCACC
AGCTGATAAAAAAATAGTCAAAAAAGCTATCAAAGCAATTGAAATTACTGAAGCGCAAGC
AAAGAAATTGAAAACTGAACCTCGAGATAAGGATGAAGTAGAAGCTGAGAATGCACTTGA
AAAATTGATTACAGAACAGACAAAATTATTATTTAAAGTTCGAGATGAAATTCAATTCCT
CAAAAAGAGCGATTTACAAAACATTCTTTTCGTAAATGATTCCGGCATGGTTAGTGGATC
TGATGCATTGATTGAACGGTGTTCTGACTTTCTTACATTCGGAGCTATCAAAAAATGTAA
GAAATGTAAGAATGGTGATATGATTTTCGCTAAATATGGTTATCGATGTAATGGAAATAT
TGATGAATGGACAATGTGTGAAAATTTTGAGGAGAAGCCTGAACGTGTTAAGTGCAAAAT
TCCAAAAGAACTTAAGGAATCGAAAGGAAACAAAAAATCTGAGAAAAACTTCTTCGCCAA
ATACAAATCCTTAGTTAAAGATCGTGCTGTTCGTCCACAAATAAAGAAGGAAATCAAGAA
AGATGAAGAAGATGGAAAA
>g3457.t2 Gene=g3457 Length=383
MEELPYKVEYAKTGRAKCRGCKINIEKDELRLAALVQSFFHDGKDCHWFHLNCFFQKHRP
KAIDDIDHFEEIRIEDQENIRQKLDATKGILLPEPKGKKKGKKRAAEDSKTAAFNATALN
DFGVEYAKSGRSACAGCGNNIMVNEVRIKKMDYTTEVGMKFGGQPFWHHVDCFAKIRGDY
NFYLDGSDLPGFSELSPADKKIVKKAIKAIEITEAQAKKLKTEPRDKDEVEAENALEKLI
TEQTKLLFKVRDEIQFLKKSDLQNILFVNDSGMVSGSDALIERCSDFLTFGAIKKCKKCK
NGDMIFAKYGYRCNGNIDEWTMCENFEEKPERVKCKIPKELKESKGNKKSEKNFFAKYKS
LVKDRAVRPQIKKEIKKDEEDGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g3457.t2 | Coils | Coil | Coil | 203 | 223 | - |
| 8 | g3457.t2 | Gene3D | G3DSA:3.30.1740.10 | - | 1 | 113 | 1.7E-29 |
| 9 | g3457.t2 | Gene3D | G3DSA:3.30.1740.10 | - | 114 | 217 | 9.9E-27 |
| 10 | g3457.t2 | Gene3D | G3DSA:1.10.20.130 | - | 218 | 291 | 3.3E-11 |
| 11 | g3457.t2 | Gene3D | G3DSA:2.20.25.630 | - | 292 | 352 | 8.0E-16 |
| 4 | g3457.t2 | PANTHER | PTHR10459 | DNA LIGASE | 47 | 365 | 3.9E-35 |
| 5 | g3457.t2 | PANTHER | PTHR10459:SF80 | POLY [ADP-RIBOSE] POLYMERASE 1 | 47 | 365 | 3.9E-35 |
| 2 | g3457.t2 | Pfam | PF00645 | Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region | 9 | 83 | 2.8E-17 |
| 1 | g3457.t2 | Pfam | PF00645 | Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region | 125 | 207 | 6.9E-14 |
| 3 | g3457.t2 | Pfam | PF08063 | PADR1 (NUC008) domain | 281 | 332 | 7.4E-18 |
| 13 | g3457.t2 | ProSitePatterns | PS00347 | Poly(ADP-ribose) polymerase zinc finger domain signature. | 18 | 53 | - |
| 18 | g3457.t2 | ProSiteProfiles | PS50064 | Poly(ADP-ribose) polymerase zinc finger domain profile. | 6 | 88 | 29.637 |
| 17 | g3457.t2 | ProSiteProfiles | PS50064 | Poly(ADP-ribose) polymerase zinc finger domain profile. | 122 | 211 | 29.818 |
| 16 | g3457.t2 | SMART | SM01336 | zf_PARP_3 | 9 | 85 | 1.0E-34 |
| 15 | g3457.t2 | SMART | SM01336 | zf_PARP_3 | 125 | 208 | 1.5E-27 |
| 14 | g3457.t2 | SMART | SM01335 | PADR1_2 | 280 | 334 | 6.9E-22 |
| 7 | g3457.t2 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 2 | 87 | 5.23E-27 |
| 6 | g3457.t2 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 119 | 219 | 1.66E-23 |
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:0008270 | zinc ion 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.
