Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA replication ATP-dependent helicase/nuclease DNA2.

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 g3379 g3379.t1 TTS g3379.t1 24987286 24987286
chr_3 g3379 g3379.t1 isoform g3379.t1 24987341 24990766
chr_3 g3379 g3379.t1 exon g3379.t1.exon1 24987341 24990064
chr_3 g3379 g3379.t1 cds g3379.t1.CDS1 24987341 24990064
chr_3 g3379 g3379.t1 exon g3379.t1.exon2 24990126 24990500
chr_3 g3379 g3379.t1 cds g3379.t1.CDS2 24990126 24990500
chr_3 g3379 g3379.t1 exon g3379.t1.exon3 24990560 24990766
chr_3 g3379 g3379.t1 cds g3379.t1.CDS3 24990560 24990766
chr_3 g3379 g3379.t1 TSS g3379.t1 24990865 24990865

Sequences

>g3379.t1 Gene=g3379 Length=3306
ATGGAAAAAAGAACAATATCAATAGTGGAAAGTCCTAAAAGTGAATCAGATAAAAATATT
AAGAAAATTAAAATTTCATTATCACCGCATAAAAATGGAGCAACTGAAAATAATGGAAAT
TTGTTAAATACAGCTGTTTTAAATAATGATATTGATGATTCATGGTTTTATAATGATGAT
GATCCTTATTTAAAAGAATTACTAGAGAAAGCGAACGAAAAGATAGAAAAACTCAATCTC
TCAAATCACAAAAGGTGCAGTGTACAAGCAATTGAGATAAATAATAAAGCTTTCGAAAAG
ATTCTTTATTTGCAAGAGAAGAAAACAAAACTAACTGGAAAATGCTGTTTGAAAGGAATA
TGGTTTGATACTGAAATATCTCAAGGCGATGTTGTGTCAGTAAAAGGGATTTGGAATGAA
GATAGAAAAATGTATCTTGTTACAAATGAAGGCGGTATTGTTGTTATTTTTCCAGACCAT
TTAGTGTCAGGAACAACGGTAGTAGGTTCTCTATTTTGTGCTCGAAAGTCGATTTTATCA
GAAAAATTTCGTGGAATTGATGATGGCAAAGATTCGATAATAATGCATATAGGTTCAATA
GTTCACGAGATACTTCAATCAGCATTAAAAGAAAATTCAACTTCATTGAACGATATAAAG
AAAATAACGAATAAAAAATTAAGCAATCCTTACATCATGCAACTACTTTATTCTTGTGAA
ATCAAATTAAAAGACTTGCAAACTCAAATTGATCCATTTATTGGAAGGATTCATGAATTT
ATGCAGGAATATATCGAAGGAAATTCTTCAAAAAAGAAATCTAATACTGATGATAATCAT
AAATTATTCAAAGGACGTATAGGTGAAGTAATTGATATTGAAGAAAATATTTGGAGCCCT
AATCTTGGATTAAAAGGAAAAATTGATGCAACTGTTTTAGTTTATGAACCAAACGATTTT
TCCAATTCATCCAGCAAATTAATGCCAATGGAAGTGAAAACAGGTCGAGCATCCTTTTCA
TTAGAACATAAAGGTCAATTATTAATCTATCAGATGATGATGCAAGACATGGGAAAACAA
ATTGATTCAGGATTATTGTTATATATTCGTGAAGGTATAATGAGTGAAATTCATCCAAAA
CGTATTGAGCAAAGTGGTCTGATTTCAATGCGTAATAGACTTGTAAAATATATGAATGCT
GATATTATTACACGAGACAAAATAATTAATTTACCAGAACCAATTACTCATCACTCTGCT
TGTGGAAATTGTCCTTATAATACTTTATGTTGTGCATTTTTAAAAAAAGAACCAAATTAT
GTACTAAAACCGAATCATCCCTTAGTTAAAATTCAAGAAAGTCATACAAATCATTTGACT
GATGAACATCTCAATTATTTTTTACATTGGTGTAATTTAATTATCTTAGAAAATAATGAA
ATTCAGAAAAGCATCAAATTAAAACACATTTGGACAAAAACTGCTGAAGAAAGGGCTATG
AAAGGAAAAGATACGTTAGCAAATCTTATTCTCAAAGATCTTGTTATGCCTCAACATGAT
GAATATATTCATACTCTTGGAACTCTGGATGATTCAACTAATTTTACTACAAAAAACTTC
AATGTCGGAGATTATCTCATTGTTAGTACGGATAAACGATGTTCGATAACAGCTGGAAGG
GTTGTAAATGTTGATTCAAATCGCATTAGTCTTAGCCTTCCTAAAGATTTAAATCATCAA
TGTACGTCTGAAAAATTCCATTTAGATAAATTCGAATCACAATCGCAATCAGTGTTCAAT
TTTACAAATATAGGTGTACTACTCGACAATGACAATGAACGCAAAATAAATCAACTTAGA
AGCATTATCATTGATAAAGAACCAGCCGTTTTTTCAAATACCTTGCCAAAATCAATTCAA
CAAAATTTAGACCAAACATTAATTAAAATGAATTCAGTTCAAAGAATGGCAGTACTGAAA
GCATTAACTTGTGAAAATTATATGCTTATTAGAGGGTTACCGGGTTCAGGCAAATCACAA
ACGCTAGTTAATCTAATTCATTTGCTTAAAATTATGAATAAGACAATATTGATTACAAGT
CATACCAATTCAGCTGTTGATAACATCTTATTACGTTTGAAAGAGCGTGGAATCACATTT
TTGCGCTTGGGCTCAATTTCAAGAATTCATCACTCATTGCGTGAATATTGCGAAACTAAG
CTAGTTGAAAATTGTAAATCTGTTGAAGAGTTGGAAAATTTATATAATTCATATCAAATT
GTTGCAATGACATGTTTAGGGGCTACTCATGCAATGTTGTCAAAAAGACGTTTTGATTTC
TGTTTAGTTGATGAAGCAACACAAATTTATCAGCCAACTGTAATTCGCCCACTCTTATCG
GCTGACAAATTTATACTCGTAGGAGATCCTGAACAATTAGCACCACTTGTAAGAAGCAAT
GATGCAAGACTGTTGGGTGCTAATGAAAGTCTTTTTGAAAGATTAAACTCAAAAGAATCA
ACATTTGTTCTTGGTCTTCAGTATCGTATGAATAAAACAATAACAAAATTAGCAAATAAT
CTCACCTACAATGGAGAATTAAAATGTGCTGATGAAATTATTGAGAAAGCTGTGATGGAA
GTACCAGATATGAATAAATTAAAAGAAAAATTATCTACTGATAAATGGTTGGCAAAAGTT
TTAACACCACATTTGGATCAAGCGTGTGCTCTTATTAACACAGGAGATGTCTATGAAATG
GCTAGAAATTATGGTGAATCACTTAAAAATAAAGATGGTAGTCAAGAATCACAAAATGAG
AAATCAAGATTATATATTAATTACTGTGAAATTGCTATTGTCACTTATATTGTTGATCTT
TTAATGGAATGCGGTGTAAAGGGTGAGTCAATCGGAATTATTGCCCCATATCGTGATCAA
GTAGAGATTTTGAAAAATGTTTTCGAATCAAATCATTCAGTGGAAGTTAATACCGTCGAT
CAATATCAAGGACGAGATAAAAAAATCATTATTTATTCATGTACGTTATCTGAAATTACA
ACAGACAAACCGAAAACATCGTCAGAAATTGAAATTCTAGAAGATCGAAGACGATTAACT
GTCGCAATAACAAGAGCCAAACACAAGTTGATAATGATTGGAGATGTTAATTGCTTAAAT
AAATATACACCATTCAGGGATCTTTTTAAGCATATGAGCAGCATTTCGAAAGTTCAAATT
CAAGATGAAAAATTTGGATTTTCATGGAACGTCATTTTAGATAAACTTAGAGTCAAATTA
ATCTAA

>g3379.t1 Gene=g3379 Length=1101
MEKRTISIVESPKSESDKNIKKIKISLSPHKNGATENNGNLLNTAVLNNDIDDSWFYNDD
DPYLKELLEKANEKIEKLNLSNHKRCSVQAIEINNKAFEKILYLQEKKTKLTGKCCLKGI
WFDTEISQGDVVSVKGIWNEDRKMYLVTNEGGIVVIFPDHLVSGTTVVGSLFCARKSILS
EKFRGIDDGKDSIIMHIGSIVHEILQSALKENSTSLNDIKKITNKKLSNPYIMQLLYSCE
IKLKDLQTQIDPFIGRIHEFMQEYIEGNSSKKKSNTDDNHKLFKGRIGEVIDIEENIWSP
NLGLKGKIDATVLVYEPNDFSNSSSKLMPMEVKTGRASFSLEHKGQLLIYQMMMQDMGKQ
IDSGLLLYIREGIMSEIHPKRIEQSGLISMRNRLVKYMNADIITRDKIINLPEPITHHSA
CGNCPYNTLCCAFLKKEPNYVLKPNHPLVKIQESHTNHLTDEHLNYFLHWCNLIILENNE
IQKSIKLKHIWTKTAEERAMKGKDTLANLILKDLVMPQHDEYIHTLGTLDDSTNFTTKNF
NVGDYLIVSTDKRCSITAGRVVNVDSNRISLSLPKDLNHQCTSEKFHLDKFESQSQSVFN
FTNIGVLLDNDNERKINQLRSIIIDKEPAVFSNTLPKSIQQNLDQTLIKMNSVQRMAVLK
ALTCENYMLIRGLPGSGKSQTLVNLIHLLKIMNKTILITSHTNSAVDNILLRLKERGITF
LRLGSISRIHHSLREYCETKLVENCKSVEELENLYNSYQIVAMTCLGATHAMLSKRRFDF
CLVDEATQIYQPTVIRPLLSADKFILVGDPEQLAPLVRSNDARLLGANESLFERLNSKES
TFVLGLQYRMNKTITKLANNLTYNGELKCADEIIEKAVMEVPDMNKLKEKLSTDKWLAKV
LTPHLDQACALINTGDVYEMARNYGESLKNKDGSQESQNEKSRLYINYCEIAIVTYIVDL
LMECGVKGESIGIIAPYRDQVEILKNVFESNHSVEVNTVDQYQGRDKKIIIYSCTLSEIT
TDKPKTSSEIEILEDRRRLTVAITRAKHKLIMIGDVNCLNKYTPFRDLFKHMSSISKVQI
QDEKFGFSWNVILDKLRVKLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3379.t1 CDD cd18041 DEXXQc_DNA2 651 849 7.42032E-90
13 g3379.t1 CDD cd18808 SF1_C_Upf1 850 1072 4.87684E-40
11 g3379.t1 Coils Coil Coil 64 84 -
9 g3379.t1 Gene3D G3DSA:3.40.50.300 - 564 846 1.6E-53
10 g3379.t1 Gene3D G3DSA:3.40.50.300 - 848 1085 1.3E-47
6 g3379.t1 PANTHER PTHR10887 DNA2/NAM7 HELICASE FAMILY 190 1073 7.1E-158
7 g3379.t1 PANTHER PTHR10887:SF433 DNA REPLICATION ATP-DEPENDENT HELICASE/NUCLEASE DNA2 190 1073 7.1E-158
3 g3379.t1 Pfam PF08696 DNA replication factor Dna2 107 313 6.9E-55
4 g3379.t1 Pfam PF01930 Domain of unknown function DUF83 321 431 7.4E-7
2 g3379.t1 Pfam PF13086 AAA domain 650 744 3.3E-13
1 g3379.t1 Pfam PF13086 AAA domain 752 819 8.7E-15
5 g3379.t1 Pfam PF13087 AAA domain 828 1056 1.3E-49
8 g3379.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 642 1057 1.26E-53

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:0033567 DNA replication, Okazaki fragment processing BP
GO:0017116 single-stranded DNA helicase activity MF
GO:0017108 5’-flap endonuclease activity MF
GO:0004386 helicase activity MF

KEGG

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