Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA polymerase alpha 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 g3813 g3813.t1 TTS g3813.t1 28159603 28159603
chr_3 g3813 g3813.t1 isoform g3813.t1 28159997 28164878
chr_3 g3813 g3813.t1 exon g3813.t1.exon1 28159997 28160205
chr_3 g3813 g3813.t1 cds g3813.t1.CDS1 28159997 28160205
chr_3 g3813 g3813.t1 exon g3813.t1.exon2 28160304 28160436
chr_3 g3813 g3813.t1 cds g3813.t1.CDS2 28160304 28160436
chr_3 g3813 g3813.t1 exon g3813.t1.exon3 28160546 28164064
chr_3 g3813 g3813.t1 cds g3813.t1.CDS3 28160546 28164064
chr_3 g3813 g3813.t1 exon g3813.t1.exon4 28164120 28164520
chr_3 g3813 g3813.t1 cds g3813.t1.CDS4 28164120 28164520
chr_3 g3813 g3813.t1 exon g3813.t1.exon5 28164584 28164784
chr_3 g3813 g3813.t1 cds g3813.t1.CDS5 28164584 28164784
chr_3 g3813 g3813.t1 exon g3813.t1.exon6 28164854 28164878
chr_3 g3813 g3813.t1 cds g3813.t1.CDS6 28164854 28164878
chr_3 g3813 g3813.t1 TSS g3813.t1 28164987 28164987

Sequences

>g3813.t1 Gene=g3813 Length=4488
ATGTCTGACGAAGAAACTGATATTGGTCTTGCTAATTCTCGATCAAAGAGAACTCGAGGA
AAGAAAAATGCTTCTGCATTTGAAAGATTAAAGGAATTAAAACAATCTGGCAGTAAAAAT
AAATGGGTAAATGAAGAATCTACAAGAATTTATGATGAGGTTGATGAAGATGAATACACA
AAAATTGTATCTGATCGTGCAGCAAATGATTGGATTGTGGACGACGTCGGTGAAGGATAT
GTTGAAGACGGAAGAGAAATTTTCGATGATGAAGAAGGAGAAGAATATGAAGTTCAGCCA
AACTCAAATAAGCGAAAAAGTCAACAAAAACGAAAAGGGAAATTACCTGATGAACCAGCA
CCTAAAAAAAAATCTCTTAAAAACTTTTTCAACAATAAAGAAACAAAAGAAAAAGAAACT
TCAAGTGTAAATGATGACAATTTATTGAAAAATATGCTTGGAGAACTCGATGGAAATTTT
AGTGTTACTAATGATTTTTTAATCGCACCTATGCCAATCAAGTCCATTAGGAAGCAAGCA
ACTGAATCTGAAATTGAAATGAAAAACTATATGGAGAGATTTGGAAAGAAAATTCAGAAA
CCAAGTAGATCAGAAGCAAATGGTGATGATATTTTAAATTCTTTGTTGAAAGAGGAACGT
AAACAAGAAAATCAAAGCCTTAAAAGATCAATGACTAAGGAATTACAAAAGGAAAATGAA
ATGTTACAGCAAATTGATGAACCTGAAGCAGTTGCTGCTCTCTCGTTGCCCCTAAAATTG
ACACCACAACAGTTGCGTGAACAAGAAGAAGCAAAAGAGATTATGGAAGTTTCTGCGATT
GATTTTGAAGATGAAGAAAATTTGATTATGCCTGAAGCAAAACCGGTTGAGAAAGAAAAA
TTTTCAACAGCAAAGATTGTAAATACAACACAGAATATGTGTATTCAAAAAAATAAGGCA
ATTTCAACGAAAACACAAAATGGTATAGATGCGACAATCTTTAATGAATTGCAAGGATCT
AATATGGAGGTTGATACAACCAACACTGTAAATAAAACAATTAATTTCAACACTGAAACA
ACTAAATTTTACTATTTGGATGCATGGACAGATATTATCAACAGACCTGGTGAAATTTAT
TTATTCGGAAAAGTTCAAGTTCCTGGTGAAGATACATACAATTCGATTTGTGTACGCATA
GAAAATGTAAATCGTCATCTTTTCTTGTTACCACGAACTCATGTTTATGACTTTAAGACA
AAAAGCCTTACGGATCAAGAAGTGTCAATTGCAGATGTCTATCAAGAATTTGATGAACGG
ATCACAAAAGAAATTAAAATTACAAGTTTCAAAAGTCGTAAAGTCTACAAGTCATTTGCA
TTTTCGGTATCTAATGTACATGTGCCACTTGAAAGCGAGTATTTAGAAGTCGTTTATTCT
GGTAAATATCCAACGCCAAACTTGAAAAATAAATATTCAACAATTGCTCACATTTTCGGC
ACAAACACTTCACCAATTGAAACTTTTATTCTTGAGCGAAAAATTAAAGGACCATGTTGG
CTCGATGTGAAAAATTTTAAAGTTGTTGAAGCTTCTTCGAGTTGGACTAAAAATCAAATA
ACATGTCCTGATATTAATTGCATTTCTGTTTCAACTGAACAAAAACCACCGCCACCATTA
ACAATTGCCACACTAAATGTAAAATGTATATTGAATTCAACAAATAATCGAAATGAAATT
GTTCAATTATCATGCTTAGTAAACGACTCCTTTCATCTCGACAAGCCCAATGAAAAACTC
GTCACACGACAATTCACTGGAATCACACGTCCATCAAATAAAAATTGGCCTATTGATATT
ATGAGTGCTATTTCAAATTTCAAGCGTTTTAAAATTTTCAAATTTGACAATGAACGTGCT
TTATTGACTTGGTTCTTGAGTGTTTATCAAAATATAGATCCCGATTTGATTGTCACATTT
GATTCAAACGATTGTCAACTCGATATCATTTGCAATCGTATCACGCTCCTAAAAATTCCT
AATTGGTCACGAATCGGAAGGCTAAAGATAAATCAGATTCCCGGTAAGAAGGTGATGGAA
TTTTTTATTGGTCGAATGGTTTGTGATGTCAAGCTTTCGGCACAAGAGCTAATCAAGAGT
CGAAGTTATGATTTAGGCACACTTTGCCAAAGGATTCTCAAAATCAAAGAAGATGAAAGG
CAAGAAATTCTGTATGACAATATTCCATATGCATACGATGCAAGCTCATCAATAATTGAA
TTTATGGAGATTAATGTACAAGATTGCATTTACATTAGCAAGCTAATGGTTGAATTGAAT
ATTTTACCACTTGCATTACAAATCACTAACATTGCTGGAAATTTAATGTCACGAACGCTT
CAAGGTGGTCGTTCTGAACGGAATGAATTCCTATTGATGCATGCATTTTACGAGAAGCAA
TATATCATTCCTGATAAGAAGATATGGAAGGACAATCAAAAGGAGGATGAGGAAGAAGGA
GAAAATGCGCACGATACTACAACACAAGTTGCAGGCACTGCTGCTGGAAAGAAAAAAGCA
GCATACACTGGTGGTCTTGTGTTAGATCCAATAAAAGGATTTTATGAGAGTTTCATTTTA
CTCATGGACTTTAATTCACTCTATCCATCAATTATACAAGAATATAACATTTGTTATACT
ACAATTGCTCCGCCAAACGATCCAAATGACTTACCCACAATACCTGATTCATCAGTTGAA
CAAGGAATTTTACCACGACAAATTCGTCGTTTAGTTGAATCTCGTCGCGATGTTAAATCA
CTGATGACGAAGCCAAATGTTACGCCAGAGTTAAAAATGCAATACAACATACGACAGTTA
GCTTTGAAATTAACGGCAAATTCGATGTACGGTTGTCTTGGATTCTCACGTTCTCGCTTT
TATGCACCACATTTGGCAGCGCTTGTTACTTTCAAAGGACGTGATATTTTAATGGCAACC
AAGACCCTCGTCGAGAAATTAAATCATAATGTAATCTATGGCGATACGGATTCAATTATG
ATTAACACAAGATCCCAAAATTACGCAGAGGTTAAAAGTATTGGTACGAATATCAAAAAG
GCAGTTAATACTGTCTATAAACACGTTGAATTAGATATTGATGGTGTCTATAAAAAACTG
CTGCTGCTAAAAAAGAAAAAGTATGCTGCCGTAGGTGTGACACAAAAGGATGACAACACA
TTAGATTATACCTATGAGTTCAAAGGTCTCGATATTGTGCGTCGTGATTGGTCTAAAATT
GCGAGTGATACGGGTAAGCTTGTGCTTAATACTTTGTTAGCTGTCGATAGTAAAAAAGAA
ATGGACGAGCGAATTGATGAGATTTTCGACATTTTAACACAACTCGGTAAAGATTTTAAT
GAGGATAAAATTCCTTTGCCAATGCTCGAGATAACAAAGCAACTTACAAAAGCACCATCA
GAATATGCAGACATGTCTTCATTGCCTCACGTCCAAGTTGCCGATCGAATGAATGTGCAA
AAGAATCGTCGCTTCAAGAAAGGCGACATGATTGATTATATCATTTGCGAAGATGGCACA
GATAATCCTGCTCCGAAACGTGGCTATCACATAGATGAAATCAAAGCTGATGCAGAAAAC
GAGACAAGAAAATTGAAAGTTGACAAATTCTATTATCTCTCACAGCAAATACATCCTGTT
ATTAGTCGTCTTTTAGAACCAATTGAAGGGATTGATAGTGCAGTTATTGCTGAAAAAATA
GGACTAGATCCAAAAGATTTTCGTAGTAAAATCAAAACAACTCGAAGTGATAATCCAGAC
AATGATCATCTTATGATAAAAACAAATGAGAAAAAGTATCGAACTTGTGAAAAATTTTCA
TTCCCGTGTGTTGCATGTAAGCAAATTCACTTTGTTGCAGCTCCGTTGAAGAAAGAAAAT
GGAAAAGTTTCATCAATATTTGAAAAGTGCACAAATACTGAATGCAAAGTTCGACCACTT
GAGTATTTGCCATTAATTAAAAATTACCTGCGTGCTGCTATTGTGAAGTCGATTCATCGA
TTTTATGAGAATTGGTTTGTTTGCGATAATCCAATGTGTAACTATAACACACAAAATTAT
TCATGGGCAATTAAAGGAAATCTTCTCTGTCTTGCATGTATGGAAGGGAATTTGCAGCGA
ACTTATACAAATGAAGATCTCAATATGCAAATCGATTATTATAATTTCATGTTTAATATT
CGCACTTATGAATCGGAAGTTTCAAATTTGAGTGGAGATGTGGTTGCTGCTTACGATATG
ATGCTTCAAACAGTTGCAGAACATTTAGAAAATTCAAACTATTTCACTGTTGAGCTCAAA
CATAAGCTTGTTGATTATGAATACAAGTTGAGTGATGAAGATCAAAAAGGCACTGATAAA
AAGTTAAACTGGAAACAGTTTTTTGCTGAAACATATGCTGCTGCATAG

>g3813.t1 Gene=g3813 Length=1495
MSDEETDIGLANSRSKRTRGKKNASAFERLKELKQSGSKNKWVNEESTRIYDEVDEDEYT
KIVSDRAANDWIVDDVGEGYVEDGREIFDDEEGEEYEVQPNSNKRKSQQKRKGKLPDEPA
PKKKSLKNFFNNKETKEKETSSVNDDNLLKNMLGELDGNFSVTNDFLIAPMPIKSIRKQA
TESEIEMKNYMERFGKKIQKPSRSEANGDDILNSLLKEERKQENQSLKRSMTKELQKENE
MLQQIDEPEAVAALSLPLKLTPQQLREQEEAKEIMEVSAIDFEDEENLIMPEAKPVEKEK
FSTAKIVNTTQNMCIQKNKAISTKTQNGIDATIFNELQGSNMEVDTTNTVNKTINFNTET
TKFYYLDAWTDIINRPGEIYLFGKVQVPGEDTYNSICVRIENVNRHLFLLPRTHVYDFKT
KSLTDQEVSIADVYQEFDERITKEIKITSFKSRKVYKSFAFSVSNVHVPLESEYLEVVYS
GKYPTPNLKNKYSTIAHIFGTNTSPIETFILERKIKGPCWLDVKNFKVVEASSSWTKNQI
TCPDINCISVSTEQKPPPPLTIATLNVKCILNSTNNRNEIVQLSCLVNDSFHLDKPNEKL
VTRQFTGITRPSNKNWPIDIMSAISNFKRFKIFKFDNERALLTWFLSVYQNIDPDLIVTF
DSNDCQLDIICNRITLLKIPNWSRIGRLKINQIPGKKVMEFFIGRMVCDVKLSAQELIKS
RSYDLGTLCQRILKIKEDERQEILYDNIPYAYDASSSIIEFMEINVQDCIYISKLMVELN
ILPLALQITNIAGNLMSRTLQGGRSERNEFLLMHAFYEKQYIIPDKKIWKDNQKEDEEEG
ENAHDTTTQVAGTAAGKKKAAYTGGLVLDPIKGFYESFILLMDFNSLYPSIIQEYNICYT
TIAPPNDPNDLPTIPDSSVEQGILPRQIRRLVESRRDVKSLMTKPNVTPELKMQYNIRQL
ALKLTANSMYGCLGFSRSRFYAPHLAALVTFKGRDILMATKTLVEKLNHNVIYGDTDSIM
INTRSQNYAEVKSIGTNIKKAVNTVYKHVELDIDGVYKKLLLLKKKKYAAVGVTQKDDNT
LDYTYEFKGLDIVRRDWSKIASDTGKLVLNTLLAVDSKKEMDERIDEIFDILTQLGKDFN
EDKIPLPMLEITKQLTKAPSEYADMSSLPHVQVADRMNVQKNRRFKKGDMIDYIICEDGT
DNPAPKRGYHIDEIKADAENETRKLKVDKFYYLSQQIHPVISRLLEPIEGIDSAVIAEKI
GLDPKDFRSKIKTTRSDNPDNDHLMIKTNEKKYRTCEKFSFPCVACKQIHFVAAPLKKEN
GKVSSIFEKCTNTECKVRPLEYLPLIKNYLRAAIVKSIHRFYENWFVCDNPMCNYNTQNY
SWAIKGNLLCLACMEGNLQRTYTNEDLNMQIDYYNFMFNIRTYESEVSNLSGDVVAAYDM
MLQTVAEHLENSNYFTVELKHKLVDYEYKLSDEDQKGTDKKLNWKQFFAETYAAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g3813.t1 CDD cd05776 DNA_polB_alpha_exo 558 787 4.57791E-76
20 g3813.t1 CDD cd05532 POLBc_alpha 856 1263 0.0
18 g3813.t1 Coils Coil Coil 173 193 -
16 g3813.t1 Gene3D G3DSA:2.40.50.730 - 362 543 6.0E-58
13 g3813.t1 Gene3D G3DSA:3.30.70.2820 - 404 516 6.0E-58
15 g3813.t1 Gene3D G3DSA:3.30.420.10 - 558 852 1.5E-92
14 g3813.t1 Gene3D G3DSA:3.90.1600.10 Palm domain of DNA polymerase 867 1071 2.6E-78
17 g3813.t1 Gene3D G3DSA:1.10.287.690 Helix hairpin bin 921 969 2.6E-78
12 g3813.t1 Gene3D G3DSA:1.10.132.60 - 1090 1278 4.7E-60
11 g3813.t1 Gene3D G3DSA:1.10.3200.20 - 1287 1452 4.1E-31
24 g3813.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
23 g3813.t1 MobiDBLite mobidb-lite consensus disorder prediction 82 127 -
25 g3813.t1 MobiDBLite mobidb-lite consensus disorder prediction 111 127 -
26 g3813.t1 MobiDBLite mobidb-lite consensus disorder prediction 832 851 -
5 g3813.t1 PANTHER PTHR45861 DNA POLYMERASE ALPHA CATALYTIC SUBUNIT 13 1461 0.0
8 g3813.t1 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 879 892 2.6E-11
7 g3813.t1 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 959 971 2.6E-11
6 g3813.t1 PRINTS PR00106 DNA-directed DNA-polymerase family B signature 1011 1019 2.6E-11
2 g3813.t1 Pfam PF12254 DNA polymerase alpha subunit p180 N terminal 28 89 3.2E-18
1 g3813.t1 Pfam PF03104 DNA polymerase family B, exonuclease domain 391 726 3.7E-36
3 g3813.t1 Pfam PF00136 DNA polymerase family B 795 1248 1.5E-114
4 g3813.t1 Pfam PF08996 DNA Polymerase alpha zinc finger 1288 1460 1.6E-28
22 g3813.t1 ProSitePatterns PS00116 DNA polymerase family B signature. 1013 1021 -
21 g3813.t1 SMART SM00486 polmehr3 558 1025 4.1E-117
10 g3813.t1 SUPERFAMILY SSF53098 Ribonuclease H-like 363 824 3.54E-64
9 g3813.t1 SUPERFAMILY SSF56672 DNA/RNA polymerases 820 1259 2.72E-107
27 g3813.t1 TIGRFAM TIGR00592 pol2: DNA polymerase (pol2) 46 1246 0.0

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:0003887 DNA-directed DNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0006260 DNA replication BP
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