General information for g2750.t1
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.t1 | TSS | g2750.t1 | 19978785 | 19978785 |
| chr_3 | g2750 | g2750.t1 | isoform | g2750.t1 | 19979210 | 19981164 |
| chr_3 | g2750 | g2750.t1 | exon | g2750.t1.exon1 | 19979210 | 19980923 |
| chr_3 | g2750 | g2750.t1 | cds | g2750.t1.CDS1 | 19979210 | 19980923 |
| chr_3 | g2750 | g2750.t1 | exon | g2750.t1.exon2 | 19980989 | 19981164 |
| chr_3 | g2750 | g2750.t1 | cds | g2750.t1.CDS2 | 19980989 | 19981164 |
| chr_3 | g2750 | g2750.t1 | TTS | g2750.t1 | 19981358 | 19981358 |
Sequences
>g2750.t1 Gene=g2750 Length=1890
ATGGAGCAAGATGAACTTTTAGACTTTGTAGAAATGAGTGATGAGATTGCCGTTCACCAA
CATCATCCAAATGTGATTCTTCATCTAGATATTGACTATTTTTACGCTCAAGTTGAAGAA
GTTTTGAAACCGGAATTGAAAACAAAGCCTTTTGGTGTAAAACAAGGCTTAAATATTGTC
ACTTGCAATTATCTAGCTCGTGAGCGAGGTGTTGGAAAATGGAAACCATTAAAAGAATGT
TTGGAAAAGTGTCCTGAATTAGTTGTTGTCAATGGCGAAGATTTGACAAATTACAAAGTA
TACTCAAAAAGAATCAGTGAAATGCTCCATGCAATGTTCGGACCAACTGAAAAAATGGGA
CTTGATGAACATTATATTGATGTGACGAAAGAAATTGAAAAAGAGATTTTGTGTGATAAA
TCTTCCACAAAACAAAAGGAACATCATTTTATTGGACCTATGTATCCCAACGAGTCAACA
TTTGATGAATGCAAGTGTCAATGTAAAGAGAGGCTTATGATTGGAACAGAAATTGCACAA
CGAGTGAGGACAAAATTGCAAGAAGAACTCAAACTTACTTGTTCAGTAGGAATAGCTCAT
AATAAATTATTATCAAAGCTTGTAGGTCAAATGAACAAGCCTAATAATCAAACAGTTTTA
GCACCTACAGCAGCAAAAGCATTCATGTGTGAACTTCGTAATCTTCGCAGTATTACAGGT
ATTGGTGAGAAGACGGCAGCTAGAATAGAAGAATTGGGCATTAAAAGTATTGAAGAACTA
CAAAATTTTGACATTTTAAAATTACAAAAGAAATTTGGAAACGATATGGCACAGCGACTT
AAAGAAATGTCTCTCGGAATAGATTCATCTGATTTTAAACCATCTGGAAAGCCAAAAACA
GTCGGTCTCGAAGACTCATTTCGTCCAATCTCAATTCGTAGTGATGCAGCAGAAAAATTT
CATGCTCTCTTATCTCGACTTATGATACAAATCCAAGATGACGGTAGAGTGCCACAGTCG
ATAAAAGTAACAGTGAGGAAATATGATCCAGCAAAGAAAAACAGTATTCGTGAGACGAAA
CAATGTACATTAGCACCATCACTCTTTCGATGTAGTGATGGTAAAATTCAATTAACAGAA
GGTGCTGAACAAAAAATTATCAAGAATGTATTGATGCTTTTCGATCGAATGGTTGATTTG
AAGCAACAGTTTAATATTACACTATTAGGGTTGTGCTTTAGCAAATTTCAAGAACAGAAA
CGTGGTCCAGCATCAATTGCAAACTACCTTATGAAGAAGCAAGATGTTGAGGTACAATCA
ATAACGAATTTAAGTAATGAAACATGTAGTTCATTTAATGATAGCTTCAGATCAAAAACT
GCTTCACCATCTTCATCATTAATGGACTTTGAAACAATATCTAACAATTCATTAGACTTA
TCGGGTTCAGAAGAATCGGAAGAGCCTTCACCTAAGAAAAGGAAAAAAATTAATTTATTA
CTTGTTGCAAGAAATCGTCGATATTCAAGTAATGATGATATTGCATCGCCAAGTAAATTA
AATGTATCAGATCTTCATTTGAATGCCTTTGATTCATGTGATTCAATAAGAACAACACCA
ACACGAATAATCTCTCCTCTTTGCTCAGAACCTATAGCGTGTTCTTCTTCTTCATTAAGA
CAAGTTGAAATTCCACCAAATATTGATCCAACAGTGTGGCAGGAGCTTCCACTAGATGTC
CAACGTGAATTAATGATGAATTGGCAGACAACTACTTCTGCTCCTTCGTCTACAACTGGC
ACAACATCCATTCCAAAAACAAAACTTAGCGGCACAAAAAAGGCAAATAACAATAATACA
TTACATAAATATTTTGTTAAAAATTCTTAA
>g2750.t1 Gene=g2750 Length=629
MEQDELLDFVEMSDEIAVHQHHPNVILHLDIDYFYAQVEEVLKPELKTKPFGVKQGLNIV
TCNYLARERGVGKWKPLKECLEKCPELVVVNGEDLTNYKVYSKRISEMLHAMFGPTEKMG
LDEHYIDVTKEIEKEILCDKSSTKQKEHHFIGPMYPNESTFDECKCQCKERLMIGTEIAQ
RVRTKLQEELKLTCSVGIAHNKLLSKLVGQMNKPNNQTVLAPTAAKAFMCELRNLRSITG
IGEKTAARIEELGIKSIEELQNFDILKLQKKFGNDMAQRLKEMSLGIDSSDFKPSGKPKT
VGLEDSFRPISIRSDAAEKFHALLSRLMIQIQDDGRVPQSIKVTVRKYDPAKKNSIRETK
QCTLAPSLFRCSDGKIQLTEGAEQKIIKNVLMLFDRMVDLKQQFNITLLGLCFSKFQEQK
RGPASIANYLMKKQDVEVQSITNLSNETCSSFNDSFRSKTASPSSSLMDFETISNNSLDL
SGSEESEEPSPKKRKKINLLLVARNRRYSSNDDIASPSKLNVSDLHLNAFDSCDSIRTTP
TRIISPLCSEPIACSSSSLRQVEIPPNIDPTVWQELPLDVQRELMMNWQTTTSAPSSTTG
TTSIPKTKLSGTKKANNNNTLHKYFVKNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2750.t1 | Gene3D | G3DSA:3.30.70.270 | - | 25 | 218 | 1.3E-60 |
| 9 | g2750.t1 | Gene3D | G3DSA:2.30.40.20 | - | 33 | 94 | 1.3E-60 |
| 10 | g2750.t1 | Gene3D | G3DSA:1.10.150.20 | 5’ to 3’ exonuclease | 221 | 297 | 2.4E-22 |
| 11 | g2750.t1 | Gene3D | G3DSA:3.30.1490.100 | - | 298 | 422 | 9.7E-37 |
| 7 | g2750.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 591 | 613 | - |
| 4 | g2750.t1 | PANTHER | PTHR46404 | DNA POLYMERASE IOTA | 17 | 509 | 5.4E-158 |
| 3 | g2750.t1 | PANTHER | PTHR46404 | DNA POLYMERASE IOTA | 515 | 595 | 5.4E-158 |
| 15 | g2750.t1 | PIRSF | PIRSF036603 | DNA_pol_eta | 18 | 151 | 1.7E-15 |
| 14 | g2750.t1 | PIRSF | PIRSF036603 | DNA_pol_eta | 140 | 498 | 8.2E-30 |
| 13 | g2750.t1 | PIRSF | PIRSF036603 | DNA_pol_eta | 512 | 629 | 2.2 |
| 1 | g2750.t1 | Pfam | PF00817 | impB/mucB/samB family | 29 | 208 | 2.5E-37 |
| 2 | g2750.t1 | Pfam | PF11799 | impB/mucB/samB family C-terminal domain | 294 | 419 | 3.5E-12 |
| 12 | g2750.t1 | ProSiteProfiles | PS50173 | UmuC domain profile. | 26 | 242 | 33.97 |
| 5 | g2750.t1 | SUPERFAMILY | SSF56672 | DNA/RNA polymerases | 24 | 296 | 2.31E-72 |
| 6 | g2750.t1 | SUPERFAMILY | SSF100879 | Lesion bypass DNA polymerase (Y-family), little finger domain | 299 | 417 | 1.37E-32 |
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 transcript has been annotated with K03510 (DNA polymerase iota)
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.
