General information for g7414.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | isoform | g7414.t1 | 23610847 | 23613567 |
| chr_2 | g7414 | g7414.t1 | exon | g7414.t1.exon1 | 23610847 | 23613412 |
| chr_2 | g7414 | g7414.t1 | cds | g7414.t1.CDS1 | 23610847 | 23613412 |
| chr_2 | g7414 | g7414.t1 | exon | g7414.t1.exon2 | 23613473 | 23613567 |
| chr_2 | g7414 | g7414.t1 | cds | g7414.t1.CDS2 | 23613473 | 23613567 |
| chr_2 | g7414 | g7414.t1 | TSS | g7414.t1 | 23614193 | 23614193 |
| chr_2 | g7414 | g7414.t1 | TTS | g7414.t1 | NA | NA |
Sequences
>g7414.t1 Gene=g7414 Length=2661
ATGTCTTTTATGCAGAAATTGGCTTTTGAAGATTTAGCAAATGTTTTTGAGCAATGTATT
TATGCTACAAGTACTTCACAACGTGATAATTACATGAAAAAATATTTTGAACAAGTTTTA
ACATTCCAGAAAATTTATATGGATGAATTCCCTAATGGAAACTCAAGCTTATTTTCTTTA
CTGAGACTTATATTATCAAATAATGAACATGAACGTGCATATGGATTACAAGAAAGAAAA
TTGCGATCATTACTAATTAAAATTTTAGCAGTTACAGGAGATAACGCAATAAAGATTGAA
AAATGCAATGAAAGTGATATTGCTGATATAGTTTTTGATATTATAAGCTCTAAAAGGAAA
TCAAAATTGTCAATAGCAGATGTCGATGATGCACTTAATGAAATATCAATTAATCAAAAA
GTTAGCGAACAAAAATATCAGTTAGAGAAACTTTACCTTAATGGTTCTGCTAAATGTCTC
AAATGGATTATTAAAATAATTCTTAAAAACATGAAACTTAAAATATCATCAGCAAAGATT
TTAGAAAAAGTTCATCCACTTGGAGGAAAGTTATTTTTAAAATATAATCATCTTTCAACT
GTGATAGAATTTATTGAGAAAGGTCAAGCAATTGAGGCAATGAAAGATGTCATAAAACCT
TTCACACCAATTAGATCTATGCTATCACAGAGATTTACCAAAGATATGAACAGTATAATA
GAGAATTTGGAATTATATAAAGAGATTAAAATGGATGGTGAAAGATTTCAATTGCATATG
CAAAATGGTGAATTTAAATATTTTTCACGTAATGCACATGATTATAGTGAAACTTTTAAT
GAGCTTATAACTCCATTAATTAAATTTAAAGTTGTTGTACATAGTGTGATACTTGATGGT
GAAATGCTTGTTTGGAATAAAGAATTGAAAAGAGTTATTACAAAAGGAGAATCAGATGTT
GATGTAAAGAAAATGCGTGATATCAATTATTACCTAAGACCATGTTTTTGTGCTTTTGAT
GTTCTTTATTTGAATGGAACAAATTTTATGAATCAACCATTTTACCATCGTTATGAAATT
CTTCGTTCACTTTTTGATGATCGAGTTGGTGTATTAATAAAAACAAACCCAATAAAAATA
AAAGATGTTGATGATTTAGTATTACAATTTAATGAAGCATTAGAAAATAATGAAGAAGGC
ATTATTTTAAAAAGAGCAGATTCATTTTATATGCCAGGTGAACGAGAGAAAGGATGGTAT
AAAATGAAAGCTGATTATTTTAATGATGAAGTTGTACAAGATTTTGATTGTGTTATCATT
GGTGGATATTTTAAAAATCCTCATACACGTGAAATGATTCAATCATATCAAATGGGAGTA
ATTGAGAAACAAAATGATGAATTTTTTTATGTTTATTCTGTTGGTGAAGTTTCTATAGGA
ATTAAAGGCATTGAACGTAAAATTTTATATGAAAAGCTTTTGCAAAGTGCATCTGATTAC
AGTGGAGAAACAATTATTGAATTTGAAAAAGGTAAAATTTTTCTTGGCAGAAAAAAGCCA
GATATCATCATACAACCACACAAATCGATTGTTCTTCAAATTCGTGTGTCTGAATTAACA
CCATCAAATGATTTTTTCACTGAATATTCATTTCGATTTCCAAGAATTGTATCAATTAGA
TATGATAAATTTTGGGATGAATCATGCACAATACAAGAATTTCAACAAATGTATAAAATT
GATGACGTAATTAATAGACGAACGATAAAAGTCAATAAACGAAATATTTATGCAGAAGAC
TTTTCTTCACCTAAGAAAAAACGTCAGCGTATTTCACTTGTTAAATCACGAGCAAGAGCA
ATTGAAAATTTTTGTCACAATTCAGAAGAAGATGTTCAACCAATTGATAACGTTTTAAAT
GGAATAGAATTTTGTGTCAGAACTTCATCACAAAATTTACCATCAGTTGATGATTTAAAA
TTACTTCTTAAATTACATGGTGCATCATTGACTGAATTTCCCCGAAAGAAGAAAACTTTT
GCAGTCGTTGCTGGTGATATTGATGAACAAATTAAAATCTACGTTAATAATAAAACTCAT
AGTATATTAAAAGTTGATTGGTTGGTGAAAAATTTTGCAAAAGATTTACCATTACTGGAC
ATTCCAAAACTTACACCATTAGATTTTTATTTTATGACTGATGAAATGTATGAAGAAAAT
TTTAAACAAAATTATGACAAATATGGTGATTCTTATTATAATGTTATTGAATCTGTTGAC
GAAATGATGAAAATTGTCAATAACATGCAGATTGAACATAAAATTTCTTCACAAGAAATA
AAAGAGTTTGAACAAGAAATCTATAGTATTGATGGAACAGAAAATTACAAAATCTTTCGA
AAATATTCAGCAAAATTTATTTATGGAAGTGAATTTAACATGAAAATGAGATGGAGTGAA
AAAGTTTTTGAATTTCTAGGAGGAAAAATTAGTCATAATCAAGATAAAAACGATTTTATA
ATTTTTGTTGATAAAGAAACTTTCAACATTCGAGAACATCCTGAATTGAAAAAATCTAAA
ATTATTGATTATCAATTTATATTAAATTCTAATGATCACAATACACTTGACAAATTAAAT
GATTACTTAATCGAATCATAA
>g7414.t1 Gene=g7414 Length=886
MSFMQKLAFEDLANVFEQCIYATSTSQRDNYMKKYFEQVLTFQKIYMDEFPNGNSSLFSL
LRLILSNNEHERAYGLQERKLRSLLIKILAVTGDNAIKIEKCNESDIADIVFDIISSKRK
SKLSIADVDDALNEISINQKVSEQKYQLEKLYLNGSAKCLKWIIKIILKNMKLKISSAKI
LEKVHPLGGKLFLKYNHLSTVIEFIEKGQAIEAMKDVIKPFTPIRSMLSQRFTKDMNSII
ENLELYKEIKMDGERFQLHMQNGEFKYFSRNAHDYSETFNELITPLIKFKVVVHSVILDG
EMLVWNKELKRVITKGESDVDVKKMRDINYYLRPCFCAFDVLYLNGTNFMNQPFYHRYEI
LRSLFDDRVGVLIKTNPIKIKDVDDLVLQFNEALENNEEGIILKRADSFYMPGEREKGWY
KMKADYFNDEVVQDFDCVIIGGYFKNPHTREMIQSYQMGVIEKQNDEFFYVYSVGEVSIG
IKGIERKILYEKLLQSASDYSGETIIEFEKGKIFLGRKKPDIIIQPHKSIVLQIRVSELT
PSNDFFTEYSFRFPRIVSIRYDKFWDESCTIQEFQQMYKIDDVINRRTIKVNKRNIYAED
FSSPKKKRQRISLVKSRARAIENFCHNSEEDVQPIDNVLNGIEFCVRTSSQNLPSVDDLK
LLLKLHGASLTEFPRKKKTFAVVAGDIDEQIKIYVNNKTHSILKVDWLVKNFAKDLPLLD
IPKLTPLDFYFMTDEMYEENFKQNYDKYGDSYYNVIESVDEMMKIVNNMQIEHKISSQEI
KEFEQEIYSIDGTENYKIFRKYSAKFIYGSEFNMKMRWSEKVFEFLGGKISHNQDKNDFI
IFVDKETFNIREHPELKKSKIIDYQFILNSNDHNTLDKLNDYLIES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g7414.t1 | CDD | cd07903 | Adenylation_DNA_ligase_IV | 215 | 428 | 5.07739E-72 |
| 13 | g7414.t1 | Coils | Coil | Coil | 766 | 786 | - |
| 10 | g7414.t1 | Gene3D | G3DSA:1.10.3260.10 | - | 1 | 211 | 2.3E-34 |
| 9 | g7414.t1 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 220 | 425 | 1.8E-53 |
| 12 | g7414.t1 | Gene3D | G3DSA:2.40.50.140 | - | 427 | 582 | 1.6E-28 |
| 11 | g7414.t1 | Gene3D | G3DSA:3.40.50.10190 | - | 642 | 753 | 2.4E-13 |
| 4 | g7414.t1 | PANTHER | PTHR45997:SF1 | DNA LIGASE 4 | 5 | 865 | 3.1E-146 |
| 5 | g7414.t1 | PANTHER | PTHR45997 | DNA LIGASE 4 | 5 | 865 | 3.1E-146 |
| 1 | g7414.t1 | Pfam | PF04675 | DNA ligase N terminus | 9 | 185 | 1.2E-23 |
| 3 | g7414.t1 | Pfam | PF01068 | ATP dependent DNA ligase domain | 227 | 423 | 4.3E-44 |
| 2 | g7414.t1 | Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 450 | 563 | 6.6E-7 |
| 15 | g7414.t1 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 335 | 462 | 23.988 |
| 16 | g7414.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 634 | 710 | 8.415 |
| 8 | g7414.t1 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 219 | 424 | 2.88E-42 |
| 7 | g7414.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 433 | 580 | 2.06E-19 |
| 6 | g7414.t1 | SUPERFAMILY | SSF52113 | BRCT domain | 638 | 710 | 1.15E-5 |
| 17 | g7414.t1 | TIGRFAM | TIGR00574 | dnl1: DNA ligase I, ATP-dependent (dnl1) | 74 | 579 | 5.8E-78 |
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:0071897 | DNA biosynthetic process | BP |
| 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 transcript has been annotated with K10777 (DNA ligase 4)
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.
