General information for g947.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA polymerase alpha subunit B.
Parent gene
- The parent gene g947 is located on chr_3: 7015577..7016605 (+ 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 | g947 | g947.t1 | TSS | g947.t1 | 7004178 | 7004178 |
| chr_3 | g947 | g947.t1 | isoform | g947.t1 | 7004259 | 7015577 |
| chr_3 | g947 | g947.t1 | exon | g947.t1.exon1 | 7004259 | 7004331 |
| chr_3 | g947 | g947.t1 | cds | g947.t1.CDS1 | 7004259 | 7004331 |
| chr_3 | g947 | g947.t1 | exon | g947.t1.exon2 | 7004385 | 7004668 |
| chr_3 | g947 | g947.t1 | cds | g947.t1.CDS2 | 7004385 | 7004668 |
| chr_3 | g947 | g947.t1 | exon | g947.t1.exon3 | 7013532 | 7013620 |
| chr_3 | g947 | g947.t1 | cds | g947.t1.CDS3 | 7013532 | 7013620 |
| chr_3 | g947 | g947.t1 | exon | g947.t1.exon4 | 7013980 | 7015023 |
| chr_3 | g947 | g947.t1 | cds | g947.t1.CDS4 | 7013980 | 7015023 |
| chr_3 | g947 | g947.t1 | exon | g947.t1.exon5 | 7015188 | 7015374 |
| chr_3 | g947 | g947.t1 | cds | g947.t1.CDS5 | 7015188 | 7015374 |
| chr_3 | g947 | g947.t1 | exon | g947.t1.exon6 | 7015431 | 7015577 |
| chr_3 | g947 | g947.t1 | cds | g947.t1.CDS6 | 7015431 | 7015577 |
| chr_3 | g947 | g947.t1 | TTS | g947.t1 | 7015654 | 7015654 |
Sequences
>g947.t1 Gene=g947 Length=1824
ATGGATATCGATAGTTTGAGAGAACAATTTGATGAACTAGGTGTTGATGCATCTCATGAC
GTTCTAGAAAAGTGCTTAGAAATTTGTCAATCATATAATTTAGAGGATCCAGTTGAATTT
GTAGAAAAATGGATGGCTTACAGCATATCAAATTTAGATGGAGCAGAACCGACTGTACAA
TATCTTTTAGAAATGGAAAATCGATTATACAAAAACCAAAATATGAAATCACAAAAGGAA
ACCAGCAAACGATCAGTTAAAGAGACATCAAATCTAAAAGTTTACAATCAGGGAAACGAT
GAAATGGATGACGATGAAAGCGAATTACTCGGATCATATGTCTGCATCACGCCAAAGAAT
GATAAAAAGTCAGCTTCAAGGCTTCATCGTGGAACTCCTGATACTTCGAAGGCCAATACA
TTTAGTCCTGTGAGCTATTCACCGTTAACTACAGCAAAAAGAACACGCATAGAATCGACA
AAAGCTGGCAATGTTTGCACATTTGGACATTACATTGCTATTTCATCAGCAAACACTAAA
CGAAATTCTCAAAATATCTTAATTAGTTTAGCAAATTTAAATGGCACACAATTTCTAGAT
GAGAAAGTTAAATATATGACAACTGCGCTTGATGATGGAGAATATGTGACAGATAGAATA
TTTAAGGTCGGTCATGAATTTTCGAAAAAAATATTGTGCGATGCAAAAGCAAAAGATATT
GCTGATGACAATGAATTTGAAGACGATCGTGTTGCTTTGAGCCATTGTGATGAGTTGTCA
CAGGAAAAAGTTCGATGTTTGGGAAAGATTTTCTGTGGTGGAAGAACAGACAAGTTAGAT
CAAAAATCATGCATATTCATTGGATTCGATGAGAACAAAATGCGAGCTGTTCAATTAGAT
TTAATGCGTTTAAAGCCTTCCGCACAAATTTTTCCCGGTGAGATTTGTATAATTAGTGGA
AGTAATCCGCGTGGAAAAACTTTTTCTGTAACTGAATTGCATGCAGAAAGAATATTACAA
AATTGTAGACTTCCGTCATCACATCGTTTAAGTGAACCGATAAATTTTGTCATTGCTTCT
GGACCATTCACTTCTGATGAAAATTTATTATTTGAATATCTCGATAAATTGATTGAAAAT
TGTCAAAATAACAAACCTGATGTACTTATACTTACTGGTGAATTTTTCAATTCAAAATCA
AAACTAATTTTCGATCTCGCAACTGAAACTGATGAACACTTTAGAAAAATGCTGGTCAGC
ATAAGTGAACGATTAGGCGAAGACACAAAAGTTGTAGTAGTCTCGTCAGTCAATGACATC
AATGGCTCAGCATGTTATCCCACAAGACCGTATGTTTTTCGTAAAGGTCTGGGAACAGCA
CAAAACATTTTCCTTGCACCCGATCCATGCATACTTGATATCAACGGTATTAAAATTGCT
GTAACGTCTGTTGATATTATTAAACATTTAGCTGATTCAGAATTTTGCATGAATGCGGGT
GGTGGTGGTGGTGATAAGATTCGTCGTTACATGAACTGTTTGTTTCATCAAAAATCCTTT
TATCCACTATTTCCGCCTAAAATAGCAACTGACATAAAATTACTTCACGAATACGCCACG
ATAAATGAAATTCCACACATATTTATTGCTCCGAGTGATATGAGATTCTTTATGAGGGAC
TTTAACGGTTGTCTTTGCGTTAATCCTGGTCGAGTAAAAAGTGGTGAAGAAAACGGTACT
TTTGCAAGAATTACTGTTCAACCACCTAAAGAACCTGTAAAAAATCTTAATTCATGGATA
TCTGGACAAATCAGTTATTTATAG
>g947.t1 Gene=g947 Length=607
MDIDSLREQFDELGVDASHDVLEKCLEICQSYNLEDPVEFVEKWMAYSISNLDGAEPTVQ
YLLEMENRLYKNQNMKSQKETSKRSVKETSNLKVYNQGNDEMDDDESELLGSYVCITPKN
DKKSASRLHRGTPDTSKANTFSPVSYSPLTTAKRTRIESTKAGNVCTFGHYIAISSANTK
RNSQNILISLANLNGTQFLDEKVKYMTTALDDGEYVTDRIFKVGHEFSKKILCDAKAKDI
ADDNEFEDDRVALSHCDELSQEKVRCLGKIFCGGRTDKLDQKSCIFIGFDENKMRAVQLD
LMRLKPSAQIFPGEICIISGSNPRGKTFSVTELHAERILQNCRLPSSHRLSEPINFVIAS
GPFTSDENLLFEYLDKLIENCQNNKPDVLILTGEFFNSKSKLIFDLATETDEHFRKMLVS
ISERLGEDTKVVVVSSVNDINGSACYPTRPYVFRKGLGTAQNIFLAPDPCILDINGIKIA
VTSVDIIKHLADSEFCMNAGGGGGDKIRRYMNCLFHQKSFYPLFPPKIATDIKLLHEYAT
INEIPHIFIAPSDMRFFMRDFNGCLCVNPGRVKSGEENGTFARITVQPPKEPVKNLNSWI
SGQISYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g947.t1 | Gene3D | G3DSA:1.10.8.530 | - | 1 | 78 | 1.1e-06 |
| 3 | g947.t1 | Gene3D | G3DSA:3.60.21.60 | - | 339 | 499 | 0.0e+00 |
| 4 | g947.t1 | Gene3D | G3DSA:3.60.21.60 | - | 511 | 602 | 0.0e+00 |
| 2 | g947.t1 | PANTHER | PTHR23061 | DNA POLYMERASE 2 ALPHA 70 KDA SUBUNIT | 3 | 593 | 0.0e+00 |
| 6 | g947.t1 | PIRSF | PIRSF018300 | DNA_pol_alpha_2 | 1 | 607 | 0.0e+00 |
| 1 | g947.t1 | Pfam | PF04042 | DNA polymerase alpha/epsilon subunit B | 356 | 557 | 0.0e+00 |
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:0006260 | DNA replication | BP |
KEGG
Orthology
- This transcript has been annotated with K02321 (DNA polymerase alpha subunit B)
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.
