Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase delta catalytic subunit.

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 g2005 g2005.t1 TSS g2005.t1 14376314 14376314
chr_3 g2005 g2005.t1 isoform g2005.t1 14376396 14379818
chr_3 g2005 g2005.t1 exon g2005.t1.exon1 14376396 14376460
chr_3 g2005 g2005.t1 cds g2005.t1.CDS1 14376396 14376460
chr_3 g2005 g2005.t1 exon g2005.t1.exon2 14376532 14376775
chr_3 g2005 g2005.t1 cds g2005.t1.CDS2 14376532 14376775
chr_3 g2005 g2005.t1 exon g2005.t1.exon3 14376834 14379818
chr_3 g2005 g2005.t1 cds g2005.t1.CDS3 14376834 14379818
chr_3 g2005 g2005.t1 TTS g2005.t1 14379883 14379883

Sequences

>g2005.t1 Gene=g2005 Length=3294
ATGAGTTCATTTGGTGGTAAACATAAGCCTAACGGTGGATATGCTGGTCCTAGCAAGAAA
TTCAAAGTGGACGATGAAGACGAAGAATATCAGAGTCAATTTGCTAATGATTTAGCCATG
ATGGATGCAGAAGATCAAGATTCAGGGGAATATGAGATCGGTGATGGCCCAGAAAATCAA
ATGCAAAATCAAAAATGGTCAAGACCTGATCTTCCCGAAATGAATCCAAATAAAGATGCA
GTAATTTTTCAACAAATTGATATTGATCATTACACAGGAAAACCAATGGCTGGTATGCCT
GGTTCTCAAATCGAACCAGTTCCAATTTTTCGAATGTATGGCATAACAATGGAAGGAAAT
TCAGTTTGTGCTCATGTTCATGGTTTTTCACCATTTCTCTATGTGCAAGCACCTGAAAAT
TTTGATAAATCTCATTTATCAGATTTCAAATCAAAACTTGATGCAATAGTTTTGAAAGAT
ATGAAGTCAAATAAAGATAATGTACAAGAAGCCATTCTTCGAGTTGAATTGGTTTACAAG
CAATCAATTCAATTTTATGTTGGTGAAGACAAGATTAAATTTATTAAAATCACTGTAGCT
TTACCAAAACTCATTGCTGCTGTAAAACGATTGCTGGATCGTGAAATCGTTATGCCTCAA
ATGAATTTTCAAGATTGTCGCTGCTTTGAAAGTAACATTGATTTCGATATTCGTTTCATG
GTTGAGACAAAAGTCGTTGGATGTAGTTGGATTGAAATTCCACCAAAAGAATGGCGAAAA
AGAGTAAAAGGAACCAAGCCTGAACCTGAAAGCCGTTGCCAATTAGAAGTTGATGTTGCA
TATGACAAATTTATTGCACACGAGCCAGAAGGAGAATGGTCAAAAGTAGCACCATTTAGA
ATTCTCAGTTTCGATATAGAATGTGCCGGCAGAAAAGGTATATTTCCAGAACCGAAATAC
GATCCTGTCATTCAAATTGCAAACATGGTTATGAGACAAGGCGAAAAAGAACCGTTCTTA
AGAAATGTATTTACTTTAGATACGTGCGCACCAATTGTAGGATCTCAAGTGCTCAGTTAT
AAGAAAGAAACAGAATTACTTGATGCTTGGAGTGCTTTTGTTCGTGAACTTGATCCTGAT
ATCATTACTGGTTATAATATTAATAATTTTGATGTACCATATCTTATCGAAAGAGCCAAA
CATCTAAAAGTCGATAAATTTGTTTATCTTGGACGAATGAAAGATGTCAAATCGGTCATA
AAAGAATCAGTTATTCAATCTAAACAAATGGGACGACGTGAAAACAAGCAAGTCAATTTT
GAAGGACGTGTTCCTTTCGATTTGCTATTTGTGCTCTTCCGCGATTACAAACTCCGATCA
TATACATTGAACGCTGTCAGTTATCACTTTCTGCAAGAACAAAAAGAAGATGTACATCAC
AGCATAATCTCAGATCTTCAAAATGGCACTGAACAAACACGTCGACGTCTTGCTATGTAT
TGTCTTAAAGATGCATATTTGCCATTGAGATTACTCAACAAATTAATGTGTATCGTCAAC
TATATGGAAATGGCTCGTGTAACGGGAGTTTCATTGGCTAGTTTACTAACTCGTGGTCAA
CAAATCAAAGTTGTCAGTCAATTATTGAGAAAAGCACGTGATGCCGGATATTTGATTCCA
ACTTACACTAGTCAAGGTGGCGATAATGAACAATTTGAAGGAGCAACAGTTATTGAACCA
AAAAGAGGCTACTATTCAGTCCCAATCGCCACTCTCGATTTTGCTTCTCTATATCCATCA
ATCATGATGGCACATAATTTGTGTTACACAACATTGTTGAAACCATCGGACAGAAAAAAA
TTGGATTTAAAAGATGAAGATGTCACGCAAACACCAGCTGGAAATTTTTTTGTTAAACCA
AATGTCAGAAAAGGTCTTTTACCAGAAATTCTTGAATCTTTGCTCAGTGCACGTAAGAAA
GCCAAAGCCGATTTGAAATCAGAAACTGATCCATTTAAAAGAAGCGTTCTCGATGGTCGA
CAGCTTGCATTGAAAATTAGTGCCAATTCAGTTTATGGATTTACAGGTGCACAAGTAGGA
AAACTGCCTTGTTTAGAAATTTCTGGAAGTGTTACAGCTTATGGTCGTACAATGATTGAA
ATGACAAAGAATGAAGTAGAGAAAAAATATACTCTATCAAATGGTTATGATTCTGACGCT
TTTGTTATTTACGGAGATACTGATTCAGTTATGGTAAACTTTGGAACAGAATCGTTACCA
CGTGCGATGGAATTAGGAAGAGAAGCAGCTGAATTTGTTAGCGAAAAATTTATTAAACCA
ATCAAACTTGAATTCGAGAAAGTTTATTATCCTTATTTACTTATTAACAAGAAACGTTAT
GCTGGATTGTATTGGACAAAACCTGAAAATTATGATAAAATGGACTGCAAAGGTATTGAA
ACTGTTCGTCGTGATAATTCACCTCTTGTTGCAAATTTAATGAATACTTGCCTACAAAAA
CTTTTGATTGAGCGCAATCCAACAGAAGCTGTTGATTATGTCAAATCAATTATCTCAGAT
TTACTTTGTAATCGAATTGATATTTCACAGTTGGTCATCACAAAAGAATTAACAAAGCAT
GACTATGCTGCAAAACAAGCACACGTTGAGCTTGCTGCAAAAATGAAGAAAAGAGATCCT
GGAAATGCACCGAAACTTGGCGATCGTGTACCATATGTTATCACAGCATCTGCTAAAAGT
ACACCAGCATATCAAAAGGCAGAAGATCCTGTTTATGTACTTGAAAATAGCATTCCAATC
GACTTTCAATATTATCTCGATAATCAGCTCTCTAAACCATTATTGAGAATTTTTGAGCCA
ATTCTTGGAGATAAAGCAGAATCAATTTTACTTCGTGGTGATCATACTCGAACAAGAATG
GGTGGAACATCAAAAGTATCAGCATTAAGTGCATTTGTACAACGTAAAGAAACATGCATT
GGTTGTAAATCTGTATTGTCAGCTGATAGATCTAAAGGAGCCTTATGCCAGCATTGCGAG
ACAAAATCTGATGAAATTTATCAAAATGAGATTGTTCAACAATGTCAACTTGAAGAAAGA
TTTTCAAGATTATGGGCAGAATGTCAACGATGTCAAGGAGCTAGAAATGAAGAAGTCTTA
TGCACAAGTCGCGATTGTCCAATCTTTTATATGCGAACAAAAGTTAGAATGGACTTGGAT
ACACAAAATAAGAGAATTATGCGATTTGGCCTTTCTGCTATAAACAACTGGTAG

>g2005.t1 Gene=g2005 Length=1097
MSSFGGKHKPNGGYAGPSKKFKVDDEDEEYQSQFANDLAMMDAEDQDSGEYEIGDGPENQ
MQNQKWSRPDLPEMNPNKDAVIFQQIDIDHYTGKPMAGMPGSQIEPVPIFRMYGITMEGN
SVCAHVHGFSPFLYVQAPENFDKSHLSDFKSKLDAIVLKDMKSNKDNVQEAILRVELVYK
QSIQFYVGEDKIKFIKITVALPKLIAAVKRLLDREIVMPQMNFQDCRCFESNIDFDIRFM
VETKVVGCSWIEIPPKEWRKRVKGTKPEPESRCQLEVDVAYDKFIAHEPEGEWSKVAPFR
ILSFDIECAGRKGIFPEPKYDPVIQIANMVMRQGEKEPFLRNVFTLDTCAPIVGSQVLSY
KKETELLDAWSAFVRELDPDIITGYNINNFDVPYLIERAKHLKVDKFVYLGRMKDVKSVI
KESVIQSKQMGRRENKQVNFEGRVPFDLLFVLFRDYKLRSYTLNAVSYHFLQEQKEDVHH
SIISDLQNGTEQTRRRLAMYCLKDAYLPLRLLNKLMCIVNYMEMARVTGVSLASLLTRGQ
QIKVVSQLLRKARDAGYLIPTYTSQGGDNEQFEGATVIEPKRGYYSVPIATLDFASLYPS
IMMAHNLCYTTLLKPSDRKKLDLKDEDVTQTPAGNFFVKPNVRKGLLPEILESLLSARKK
AKADLKSETDPFKRSVLDGRQLALKISANSVYGFTGAQVGKLPCLEISGSVTAYGRTMIE
MTKNEVEKKYTLSNGYDSDAFVIYGDTDSVMVNFGTESLPRAMELGREAAEFVSEKFIKP
IKLEFEKVYYPYLLINKKRYAGLYWTKPENYDKMDCKGIETVRRDNSPLVANLMNTCLQK
LLIERNPTEAVDYVKSIISDLLCNRIDISQLVITKELTKHDYAAKQAHVELAAKMKKRDP
GNAPKLGDRVPYVITASAKSTPAYQKAEDPVYVLENSIPIDFQYYLDNQLSKPLLRIFEP
ILGDKAESILLRGDHTRTRMGGTSKVSALSAFVQRKETCIGCKSVLSADRSKGALCQHCE
TKSDEIYQNEIVQQCQLEERFSRLWAECQRCQGARNEEVLCTSRDCPIFYMRTKVRMDLD
TQNKRIMRFGLSAINNW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g2005.t1 CDD cd05777 DNA_polB_delta_exo 293 522 1.9334E-157
16 g2005.t1 CDD cd05533 POLBc_delta 570 962 0.0
14 g2005.t1 Gene3D G3DSA:3.30.342.10 DNA Polymerase 109 560 4.4E-174
13 g2005.t1 Gene3D G3DSA:3.30.420.10 - 300 528 4.4E-174
12 g2005.t1 Gene3D G3DSA:3.90.1600.10 Palm domain of DNA polymerase 572 801 2.6E-82
15 g2005.t1 Gene3D G3DSA:1.10.287.690 Helix hairpin bin 645 697 2.6E-82
11 g2005.t1 Gene3D G3DSA:1.10.132.60 - 818 971 2.0E-48
20 g2005.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 30 -
4 g2005.t1 PANTHER PTHR10322:SF23 DNA POLYMERASE DELTA CATALYTIC SUBUNIT 79 1090 0.0
5 g2005.t1 PANTHER PTHR10322 DNA POLYMERASE CATALYTIC SUBUNIT 79 1090 0.0
7 g2005.t1 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 589 602 2.2E-11
8 g2005.t1 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 681 693 2.2E-11
6 g2005.t1 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 742 750 2.2E-11
1 g2005.t1 Pfam PF03104 DNA polymerase family B, exonuclease domain 116 466 4.1E-75
2 g2005.t1 Pfam PF00136 DNA polymerase family B 532 961 5.3E-149
3 g2005.t1 Pfam PF14260 C4-type zinc-finger of DNA polymerase delta 999 1072 9.6E-16
18 g2005.t1 ProSitePatterns PS00116 DNA polymerase family B signature. 744 752 -
19 g2005.t1 SMART SM00486 polmehr3 297 756 2.5E-167
10 g2005.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 103 536 7.09E-101
9 g2005.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 556 969 4.39E-131
21 g2005.t1 TIGRFAM TIGR00592 pol2: DNA polymerase (pol2) 552 959 8.4E-86

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:0003887 DNA-directed DNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0000166 nucleotide binding MF
GO:0003676 nucleic acid 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