General information for g3379.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA replication ATP-dependent helicase/nuclease DNA2.
Parent gene
- The parent gene g3379 is located on chr_3: 24987341..24990766 (- 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 | g3379 | g3379.t2 | TTS | g3379.t2 | 24987286 | 24987286 |
| chr_3 | g3379 | g3379.t2 | isoform | g3379.t2 | 24987341 | 24988443 |
| chr_3 | g3379 | g3379.t2 | exon | g3379.t2.exon1 | 24987341 | 24988443 |
| chr_3 | g3379 | g3379.t2 | cds | g3379.t2.CDS1 | 24987341 | 24988360 |
| chr_3 | g3379 | g3379.t2 | TSS | g3379.t2 | 24988424 | 24988424 |
Sequences
>g3379.t2 Gene=g3379 Length=1103
AATATTGCGAAACTAAGCTAGTTGAAAATTGTAAATCTGTTGAAGAGTTGGAAAATTTAT
ATAATTCATATCAAATTGTTGCAATGACATGTTTAGGGGCTACTCATGCAATGTTGTCAA
AAAGACGTTTTGATTTCTGTTTAGTTGATGAAGCAACACAAATTTATCAGCCAACTGTAA
TTCGCCCACTCTTATCGGCTGACAAATTTATACTCGTAGGAGATCCTGAACAATTAGCAC
CACTTGTAAGAAGCAATGATGCAAGACTGTTGGGTGCTAATGAAAGTCTTTTTGAAAGAT
TAAACTCAAAAGAATCAACATTTGTTCTTGGTCTTCAGTATCGTATGAATAAAACAATAA
CAAAATTAGCAAATAATCTCACCTACAATGGAGAATTAAAATGTGCTGATGAAATTATTG
AGAAAGCTGTGATGGAAGTACCAGATATGAATAAATTAAAAGAAAAATTATCTACTGATA
AATGGTTGGCAAAAGTTTTAACACCACATTTGGATCAAGCGTGTGCTCTTATTAACACAG
GAGATGTCTATGAAATGGCTAGAAATTATGGTGAATCACTTAAAAATAAAGATGGTAGTC
AAGAATCACAAAATGAGAAATCAAGATTATATATTAATTACTGTGAAATTGCTATTGTCA
CTTATATTGTTGATCTTTTAATGGAATGCGGTGTAAAGGGTGAGTCAATCGGAATTATTG
CCCCATATCGTGATCAAGTAGAGATTTTGAAAAATGTTTTCGAATCAAATCATTCAGTGG
AAGTTAATACCGTCGATCAATATCAAGGACGAGATAAAAAAATCATTATTTATTCATGTA
CGTTATCTGAAATTACAACAGACAAACCGAAAACATCGTCAGAAATTGAAATTCTAGAAG
ATCGAAGACGATTAACTGTCGCAATAACAAGAGCCAAACACAAGTTGATAATGATTGGAG
ATGTTAATTGCTTAAATAAATATACACCATTCAGGGATCTTTTTAAGCATATGAGCAGCA
TTTCGAAAGTTCAAATTCAAGATGAAAAATTTGGATTTTCATGGAACGTCATTTTAGATA
AACTTAGAGTCAAATTAATCTAA
>g3379.t2 Gene=g3379 Length=339
MTCLGATHAMLSKRRFDFCLVDEATQIYQPTVIRPLLSADKFILVGDPEQLAPLVRSNDA
RLLGANESLFERLNSKESTFVLGLQYRMNKTITKLANNLTYNGELKCADEIIEKAVMEVP
DMNKLKEKLSTDKWLAKVLTPHLDQACALINTGDVYEMARNYGESLKNKDGSQESQNEKS
RLYINYCEIAIVTYIVDLLMECGVKGESIGIIAPYRDQVEILKNVFESNHSVEVNTVDQY
QGRDKKIIIYSCTLSEITTDKPKTSSEIEILEDRRRLTVAITRAKHKLIMIGDVNCLNKY
TPFRDLFKHMSSISKVQIQDEKFGFSWNVILDKLRVKLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3379.t2 | CDD | cd18808 | SF1_C_Upf1 | 88 | 310 | 0 |
| 7 | g3379.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 85 | 0 |
| 6 | g3379.t2 | Gene3D | G3DSA:3.40.50.300 | - | 86 | 323 | 0 |
| 3 | g3379.t2 | PANTHER | PTHR10887 | DNA2/NAM7 HELICASE FAMILY | 2 | 311 | 0 |
| 4 | g3379.t2 | PANTHER | PTHR10887:SF433 | DNA REPLICATION ATP-DEPENDENT HELICASE/NUCLEASE DNA2 | 2 | 311 | 0 |
| 1 | g3379.t2 | Pfam | PF13086 | AAA domain | 2 | 57 | 0 |
| 2 | g3379.t2 | Pfam | PF13087 | AAA domain | 66 | 294 | 0 |
| 5 | g3379.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 13 | 295 | 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: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
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
