General information for g7414.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative DNA ligase 4.
Parent gene
- The parent gene g7414 is located on chr_2: 23610847..23613567 (- 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_2 | g7414 | g7414.t3 | isoform | g7414.t3 | 23610614 | 23612531 |
| chr_2 | g7414 | g7414.t3 | exon | g7414.t3.exon1 | 23610614 | 23612531 |
| chr_2 | g7414 | g7414.t3 | cds | g7414.t3.CDS1 | 23610847 | 23612460 |
| chr_2 | g7414 | g7414.t3 | TSS | g7414.t3 | NA | NA |
| chr_2 | g7414 | g7414.t3 | TTS | g7414.t3 | NA | NA |
Sequences
>g7414.t3 Gene=g7414 Length=1918
GTGATATCAATTATTACCTAAGACCATGTTTTTGTGCTTTTGATGTTCTTTATTTGAATG
GAACAAATTTTATGAATCAACCATTTTACCATCGTTATGAAATTCTTCGTTCACTTTTTG
ATGATCGAGTTGGTGTATTAATAAAAACAAACCCAATAAAAATAAAAGATGTTGATGATT
TAGTATTACAATTTAATGAAGCATTAGAAAATAATGAAGAAGGCATTATTTTAAAAAGAG
CAGATTCATTTTATATGCCAGGTGAACGAGAGAAAGGATGGTATAAAATGAAAGCTGATT
ATTTTAATGATGAAGTTGTACAAGATTTTGATTGTGTTATCATTGGTGGATATTTTAAAA
ATCCTCATACACGTGAAATGATTCAATCATATCAAATGGGAGTAATTGAGAAACAAAATG
ATGAATTTTTTTATGTTTATTCTGTTGGTGAAGTTTCTATAGGAATTAAAGGCATTGAAC
GTAAAATTTTATATGAAAAGCTTTTGCAAAGTGCATCTGATTACAGTGGAGAAACAATTA
TTGAATTTGAAAAAGGTAAAATTTTTCTTGGCAGAAAAAAGCCAGATATCATCATACAAC
CACACAAATCGATTGTTCTTCAAATTCGTGTGTCTGAATTAACACCATCAAATGATTTTT
TCACTGAATATTCATTTCGATTTCCAAGAATTGTATCAATTAGATATGATAAATTTTGGG
ATGAATCATGCACAATACAAGAATTTCAACAAATGTATAAAATTGATGACGTAATTAATA
GACGAACGATAAAAGTCAATAAACGAAATATTTATGCAGAAGACTTTTCTTCACCTAAGA
AAAAACGTCAGCGTATTTCACTTGTTAAATCACGAGCAAGAGCAATTGAAAATTTTTGTC
ACAATTCAGAAGAAGATGTTCAACCAATTGATAACGTTTTAAATGGAATAGAATTTTGTG
TCAGAACTTCATCACAAAATTTACCATCAGTTGATGATTTAAAATTACTTCTTAAATTAC
ATGGTGCATCATTGACTGAATTTCCCCGAAAGAAGAAAACTTTTGCAGTCGTTGCTGGTG
ATATTGATGAACAAATTAAAATCTACGTTAATAATAAAACTCATAGTATATTAAAAGTTG
ATTGGTTGGTGAAAAATTTTGCAAAAGATTTACCATTACTGGACATTCCAAAACTTACAC
CATTAGATTTTTATTTTATGACTGATGAAATGTATGAAGAAAATTTTAAACAAAATTATG
ACAAATATGGTGATTCTTATTATAATGTTATTGAATCTGTTGACGAAATGATGAAAATTG
TCAATAACATGCAGATTGAACATAAAATTTCTTCACAAGAAATAAAAGAGTTTGAACAAG
AAATCTATAGTATTGATGGAACAGAAAATTACAAAATCTTTCGAAAATATTCAGCAAAAT
TTATTTATGGAAGTGAATTTAACATGAAAATGAGATGGAGTGAAAAAGTTTTTGAATTTC
TAGGAGGAAAAATTAGTCATAATCAAGATAAAAACGATTTTATAATTTTTGTTGATAAAG
AAACTTTCAACATTCGAGAACATCCTGAATTGAAAAAATCTAAAATTATTGATTATCAAT
TTATATTAAATTCTAATGATCACAATACACTTGACAAATTAAATGATTACTTAATCGAAT
CATAATTGTTGATACAAATTTTATTTTAAATCATCATATTAAATAATATTTTTACACAAG
ATAACAGAATTCTACATTATTTTAATGAAAATTAATCAAGCATTAAATGGAGTGCTCTGA
AAAATAAACCAACTGTTCTTGAAAAATAAACCAACTGTATTCTCCAAGCAAACAGTTAAC
AAAAACTACAAATACAAAAGATTTTATTAAAAAACACAAAATAAAATAACTAAAATAC
>g7414.t3 Gene=g7414 Length=537
MNQPFYHRYEILRSLFDDRVGVLIKTNPIKIKDVDDLVLQFNEALENNEEGIILKRADSF
YMPGEREKGWYKMKADYFNDEVVQDFDCVIIGGYFKNPHTREMIQSYQMGVIEKQNDEFF
YVYSVGEVSIGIKGIERKILYEKLLQSASDYSGETIIEFEKGKIFLGRKKPDIIIQPHKS
IVLQIRVSELTPSNDFFTEYSFRFPRIVSIRYDKFWDESCTIQEFQQMYKIDDVINRRTI
KVNKRNIYAEDFSSPKKKRQRISLVKSRARAIENFCHNSEEDVQPIDNVLNGIEFCVRTS
SQNLPSVDDLKLLLKLHGASLTEFPRKKKTFAVVAGDIDEQIKIYVNNKTHSILKVDWLV
KNFAKDLPLLDIPKLTPLDFYFMTDEMYEENFKQNYDKYGDSYYNVIESVDEMMKIVNNM
QIEHKISSQEIKEFEQEIYSIDGTENYKIFRKYSAKFIYGSEFNMKMRWSEKVFEFLGGK
ISHNQDKNDFIIFVDKETFNIREHPELKKSKIIDYQFILNSNDHNTLDKLNDYLIES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g7414.t3 | Coils | Coil | Coil | 417 | 437 | - |
| 8 | g7414.t3 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 1 | 76 | 1.8E-14 |
| 10 | g7414.t3 | Gene3D | G3DSA:2.40.50.140 | - | 78 | 233 | 6.6E-29 |
| 9 | g7414.t3 | Gene3D | G3DSA:3.40.50.10190 | - | 293 | 404 | 1.1E-13 |
| 3 | g7414.t3 | PANTHER | PTHR45997:SF1 | DNA LIGASE 4 | 1 | 459 | 3.5E-72 |
| 4 | g7414.t3 | PANTHER | PTHR45997 | DNA LIGASE 4 | 1 | 459 | 3.5E-72 |
| 2 | g7414.t3 | Pfam | PF01068 | ATP dependent DNA ligase domain | 1 | 74 | 3.6E-11 |
| 1 | g7414.t3 | Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 101 | 214 | 3.0E-7 |
| 12 | g7414.t3 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 1 | 113 | 18.471 |
| 13 | g7414.t3 | ProSiteProfiles | PS50172 | BRCT domain profile. | 285 | 361 | 8.415 |
| 7 | g7414.t3 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 2 | 74 | 2.13E-13 |
| 6 | g7414.t3 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 84 | 231 | 8.57E-20 |
| 5 | g7414.t3 | SUPERFAMILY | SSF52113 | BRCT domain | 282 | 361 | 1.16E-5 |
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:0003677 | DNA binding | MF |
| GO:0006281 | DNA repair | BP |
| GO:0005524 | ATP binding | MF |
| GO:0051103 | DNA ligation involved in DNA repair | BP |
| GO:0003910 | DNA ligase (ATP) activity | MF |
| GO:0006310 | DNA recombination | BP |
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.
