Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase iota.

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 g2750 g2750.t10 TSS g2750.t10 19978785 19978785
chr_3 g2750 g2750.t10 isoform g2750.t10 19978926 19981164
chr_3 g2750 g2750.t10 exon g2750.t10.exon1 19978926 19979088
chr_3 g2750 g2750.t10 exon g2750.t10.exon2 19979204 19980923
chr_3 g2750 g2750.t10 cds g2750.t10.CDS1 19979210 19980923
chr_3 g2750 g2750.t10 exon g2750.t10.exon3 19980989 19981164
chr_3 g2750 g2750.t10 cds g2750.t10.CDS2 19980989 19981164
chr_3 g2750 g2750.t10 TTS g2750.t10 19981358 19981358

Sequences

>g2750.t10 Gene=g2750 Length=2059
GAAAAATTTCAAGTGAAAACAAGAAAGTGGACAAAACGTAAACAAAATCTCATTTTATTA
TAAAAATGTGCTAAAAACAGTAATAAGATTAAGACTTTCAATAATTCTTCTAAAAATCCT
ACCTAAATGTAAATAAAAACATTAAAAACTCTCTTATTCTCAGCAAAAAATGGAGCAAGA
TGAACTTTTAGACTTTGTAGAAATGAGTGATGAGATTGCCGTTCACCAACATCATCCAAA
TGTGATTCTTCATCTAGATATTGACTATTTTTACGCTCAAGTTGAAGAAGTTTTGAAACC
GGAATTGAAAACAAAGCCTTTTGGTGTAAAACAAGGCTTAAATATTGTCACTTGCAATTA
TCTAGCTCGTGAGCGAGGTGTTGGAAAATGGAAACCATTAAAAGAATGTTTGGAAAAGTG
TCCTGAATTAGTTGTTGTCAATGGCGAAGATTTGACAAATTACAAAGTATACTCAAAAAG
AATCAGTGAAATGCTCCATGCAATGTTCGGACCAACTGAAAAAATGGGACTTGATGAACA
TTATATTGATGTGACGAAAGAAATTGAAAAAGAGATTTTGTGTGATAAATCTTCCACAAA
ACAAAAGGAACATCATTTTATTGGACCTATGTATCCCAACGAGTCAACATTTGATGAATG
CAAGTGTCAATGTAAAGAGAGGCTTATGATTGGAACAGAAATTGCACAACGAGTGAGGAC
AAAATTGCAAGAAGAACTCAAACTTACTTGTTCAGTAGGAATAGCTCATAATAAATTATT
ATCAAAGCTTGTAGGTCAAATGAACAAGCCTAATAATCAAACAGTTTTAGCACCTACAGC
AGCAAAAGCATTCATGTGTGAACTTCGTAATCTTCGCAGTATTACAGGTATTGGTGAGAA
GACGGCAGCTAGAATAGAAGAATTGGGCATTAAAAGTATTGAAGAACTACAAAATTTTGA
CATTTTAAAATTACAAAAGAAATTTGGAAACGATATGGCACAGCGACTTAAAGAAATGTC
TCTCGGAATAGATTCATCTGATTTTAAACCATCTGGAAAGCCAAAAACAGTCGGTCTCGA
AGACTCATTTCGTCCAATCTCAATTCGTAGTGATGCAGCAGAAAAATTTCATGCTCTCTT
ATCTCGACTTATGATACAAATCCAAGATGACGGTAGAGTGCCACAGTCGATAAAAGTAAC
AGTGAGGAAATATGATCCAGCAAAGAAAAACAGTATTCGTGAGACGAAACAATGTACATT
AGCACCATCACTCTTTCGATGTAGTGATGGTAAAATTCAATTAACAGAAGGTGCTGAACA
AAAAATTATCAAGAATGTATTGATGCTTTTCGATCGAATGGTTGATTTGAAGCAACAGTT
TAATATTACACTATTAGGGTTGTGCTTTAGCAAATTTCAAGAACAGAAACGTGGTCCAGC
ATCAATTGCAAACTACCTTATGAAGAAGCAAGATGTTGAGGTACAATCAATAACGAATTT
AAGTAATGAAACATGTAGTTCATTTAATGATAGCTTCAGATCAAAAACTGCTTCACCATC
TTCATCATTAATGGACTTTGAAACAATATCTAACAATTCATTAGACTTATCGGGTTCAGA
AGAATCGGAAGAGCCTTCACCTAAGAAAAGGAAAAAAATTAATTTATTACTTGTTGCAAG
AAATCGTCGATATTCAAGTAATGATGATATTGCATCGCCAAGTAAATTAAATGTATCAGA
TCTTCATTTGAATGCCTTTGATTCATGTGATTCAATAAGAACAACACCAACACGAATAAT
CTCTCCTCTTTGCTCAGAACCTATAGCGTGTTCTTCTTCTTCATTAAGACAAGTTGAAAT
TCCACCAAATATTGATCCAACAGTGTGGCAGGAGCTTCCACTAGATGTCCAACGTGAATT
AATGATGAATTGGCAGACAACTACTTCTGCTCCTTCGTCTACAACTGGCACAACATCCAT
TCCAAAAACAAAACTTAGCGGCACAAAAAAGGCAAATAACAATAATACATTACATAAATA
TTTTGTTAAAAATTCTTAA

>g2750.t10 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.t10 Gene3D G3DSA:3.30.70.270 - 25 218 1.3E-60
9 g2750.t10 Gene3D G3DSA:2.30.40.20 - 33 94 1.3E-60
10 g2750.t10 Gene3D G3DSA:1.10.150.20 5’ to 3’ exonuclease 221 297 2.4E-22
11 g2750.t10 Gene3D G3DSA:3.30.1490.100 - 298 422 9.7E-37
7 g2750.t10 MobiDBLite mobidb-lite consensus disorder prediction 591 613 -
4 g2750.t10 PANTHER PTHR46404 DNA POLYMERASE IOTA 17 509 5.4E-158
3 g2750.t10 PANTHER PTHR46404 DNA POLYMERASE IOTA 515 595 5.4E-158
15 g2750.t10 PIRSF PIRSF036603 DNA_pol_eta 18 151 1.7E-15
14 g2750.t10 PIRSF PIRSF036603 DNA_pol_eta 140 498 8.3E-30
13 g2750.t10 PIRSF PIRSF036603 DNA_pol_eta 512 629 2.2
1 g2750.t10 Pfam PF00817 impB/mucB/samB family 29 208 2.5E-37
2 g2750.t10 Pfam PF11799 impB/mucB/samB family C-terminal domain 294 419 3.5E-12
12 g2750.t10 ProSiteProfiles PS50173 UmuC domain profile. 26 242 33.97
5 g2750.t10 SUPERFAMILY SSF56672 DNA/RNA polymerases 24 296 2.31E-72
6 g2750.t10 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

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