General information for g2750.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA polymerase iota.
Parent gene
- The parent gene g2750 is located on chr_3: 19979775..19981418 (+ 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 | g2750 | g2750.t12 | TSS | g2750.t12 | 19978785 | 19978785 |
| chr_3 | g2750 | g2750.t12 | isoform | g2750.t12 | 19979775 | 19981418 |
| chr_3 | g2750 | g2750.t12 | exon | g2750.t12.exon1 | 19979775 | 19981098 |
| chr_3 | g2750 | g2750.t12 | cds | g2750.t12.CDS1 | 19979840 | 19980943 |
| chr_3 | g2750 | g2750.t12 | exon | g2750.t12.exon2 | 19981410 | 19981418 |
| chr_3 | g2750 | g2750.t12 | TTS | g2750.t12 | NA | NA |
Sequences
>g2750.t12 Gene=g2750 Length=1333
AACTCAAACTTACTTGTTCAGTAGGAATAGCTCATAATAAATTATTATCAAAGCTTGTAG
GTCAAATGAACAAGCCTAATAATCAAACAGTTTTAGCACCTACAGCAGCAAAAGCATTCA
TGTGTGAACTTCGTAATCTTCGCAGTATTACAGGTATTGGTGAGAAGACGGCAGCTAGAA
TAGAAGAATTGGGCATTAAAAGTATTGAAGAACTACAAAATTTTGACATTTTAAAATTAC
AAAAGAAATTTGGAAACGATATGGCACAGCGACTTAAAGAAATGTCTCTCGGAATAGATT
CATCTGATTTTAAACCATCTGGAAAGCCAAAAACAGTCGGTCTCGAAGACTCATTTCGTC
CAATCTCAATTCGTAGTGATGCAGCAGAAAAATTTCATGCTCTCTTATCTCGACTTATGA
TACAAATCCAAGATGACGGTAGAGTGCCACAGTCGATAAAAGTAACAGTGAGGAAATATG
ATCCAGCAAAGAAAAACAGTATTCGTGAGACGAAACAATGTACATTAGCACCATCACTCT
TTCGATGTAGTGATGGTAAAATTCAATTAACAGAAGGTGCTGAACAAAAAATTATCAAGA
ATGTATTGATGCTTTTCGATCGAATGGTTGATTTGAAGCAACAGTTTAATATTACACTAT
TAGGGTTGTGCTTTAGCAAATTTCAAGAACAGAAACGTGGTCCAGCATCAATTGCAAACT
ACCTTATGAAGAAGCAAGATGTTGAGGTACAATCAATAACGAATTTAAGTAATGAAACAT
GTAGTTCATTTAATGATAGCTTCAGATCAAAAACTGCTTCACCATCTTCATCATTAATGG
ACTTTGAAACAATATCTAACAATTCATTAGACTTATCGGGTTCAGAAGAATCGGAAGAGC
CTTCACCTAAGAAAAGGAAAAAAATTAATTTATTACTTGTTGCAAGAAATCGTCGATATT
CAAGTAATGATGATATTGCATCGCCAAGTAAATTAAATGTATCAGATCTTCATTTGAATG
CCTTTGATTCATGTGATTCAATAAGAACAACACCAACACGAATAATCTCTCCTCTTTGCT
CAGAACCTATAGCGTGTTCTTCTTCTTCATTAAGACAAGTTGAAATTCCACCAAATATTG
ATCCAACAGGTTTGTCTATGTTATATTAAATATAATAGACATACCATGAATGTTGTGTTG
ATTTTCCTTTATAGTGTGGCAGGAGCTTCCACTAGATGTCCAACGTGAATTAATGATGAA
TTGGCAGACAACTACTTCTGCTCCTTCGTCTACAACTGGCACAACATCCATTCCAAAAAC
AAAACTCTTAAGA
>g2750.t12 Gene=g2750 Length=367
MNKPNNQTVLAPTAAKAFMCELRNLRSITGIGEKTAARIEELGIKSIEELQNFDILKLQK
KFGNDMAQRLKEMSLGIDSSDFKPSGKPKTVGLEDSFRPISIRSDAAEKFHALLSRLMIQ
IQDDGRVPQSIKVTVRKYDPAKKNSIRETKQCTLAPSLFRCSDGKIQLTEGAEQKIIKNV
LMLFDRMVDLKQQFNITLLGLCFSKFQEQKRGPASIANYLMKKQDVEVQSITNLSNETCS
SFNDSFRSKTASPSSSLMDFETISNNSLDLSGSEESEEPSPKKRKKINLLLVARNRRYSS
NDDIASPSKLNVSDLHLNAFDSCDSIRTTPTRIISPLCSEPIACSSSSLRQVEIPPNIDP
TGLSMLY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g2750.t12 | Gene3D | G3DSA:1.10.150.20 | 5’ to 3’ exonuclease | 11 | 87 | 0 |
| 6 | g2750.t12 | Gene3D | G3DSA:3.30.1490.100 | - | 88 | 212 | 0 |
| 2 | g2750.t12 | PANTHER | PTHR46404 | DNA POLYMERASE IOTA | 2 | 316 | 0 |
| 1 | g2750.t12 | Pfam | PF11799 | impB/mucB/samB family C-terminal domain | 84 | 209 | 0 |
| 3 | g2750.t12 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 1 | 86 | 0 |
| 4 | g2750.t12 | SUPERFAMILY | SSF100879 | Lesion bypass DNA polymerase (Y-family), little finger domain | 89 | 207 | 0 |
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:0006281 | DNA repair | BP |
| GO:0003684 | damaged DNA 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.
