General information for g2448.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA ligase 4.
Parent gene
- The parent gene g2448 is located on chr_3: 18020524..18023081 (+ 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 | g2448 | g2448.t2 | TSS | g2448.t2 | 18020284 | 18020284 |
| chr_3 | g2448 | g2448.t2 | isoform | g2448.t2 | 18020524 | 18023081 |
| chr_3 | g2448 | g2448.t2 | exon | g2448.t2.exon1 | 18020524 | 18023081 |
| chr_3 | g2448 | g2448.t2 | cds | g2448.t2.CDS1 | 18020928 | 18023081 |
| chr_3 | g2448 | g2448.t2 | TTS | g2448.t2 | 18023099 | 18023099 |
Sequences
>g2448.t2 Gene=g2448 Length=2558
TTGAACAAGTTTTTAAATTACAAAAAAGATATTTGAGTGAATCTCCTAATGGTAACTCAA
GTGTGTATCCTTTACTGCGGCTTATTCTTTCAACTGATGAGCATGAACGTGCTTACGGAT
TACAGGAAATAAGATTACGTCAGCTCTTAATTAAAACTTTAGCAGTTACAGGAGATAATG
CAAAGAAAATAGAGGAATGCAATGAAGACGATATTGGTGAGAAGGTTTGTGAGATAATCG
GTTCAAATAAAATATCAAAATTGTCAATAGCAGACGTAGATGATGCACTTAATCAAATTT
CAAATAATCAAAAAATTAACGAACAAAAATTGCAACTTGAAAAGCTTTATTTAAAAGGAT
CTGGTAAATGTCTCAAATGGATCGTCAAGATAATTCTTAAAAACATGAAACTCAAAATAT
CACCTGCAAAGATTCTAGAGAAAGTTCATCCGCTTGGAGGAAAACTTTTTACCAAATACA
ATCATCTTTCAACTGTGATAGAATTTATTGAAAAAGGACAAGCGATTGAAGCAATGAAAG
ATGTTATTAAGCCTTTTACACCGATCAGAGCTATGCTATCGCAAAAATTTTCTATAGACA
TGAACAAGATGTTAGAGAAATTTGAACTATATCAAGAGATAAAAATGGATGGTGAACGAT
TTCAGTTGCATATGGAAAATGGAGAATACAAATATTTTTCACGTAATGCACACGATTTTA
GTCAATGTTTTAATCAGTTCATAACTCCATTAATTAAATACAAAGTAGTAGTGCATAGTG
TGATTCTCGATGGTGAAATGATTATTTGGAATAAAGAATTGAGACGATTTGTTACAAAAG
GAGAGACTGATATGGATGTAAAAAAGATGAAAGATATCAATCATAATATGCGACCATGCT
TTTGTGCCTTTGATGTGCTTTATTTAAATGGAACAAGTTTTATCGATCAGCCATTTTATC
GTCGTTATGAAATTCTTCATTCACTTTTTGATGATCGTGTTGGAGTGTTGATAAAAACAA
ATCCAGTTAAAATAAGAGATGTTGAACATTTAGTATCACAATTCAACAAAGCATTAGATA
ACAATGAGGAAGGTATCATTCTAAAGAAAGCAGATTCAACCTACATGCCAGGAGAACGAG
ATAAAGGAGGATGGTACAAAATGAAAGCTGATTATTTCAATGATGAAGTTGTGGAAGATT
TTGATTGCGTCATCATTGGTGGATATTTTAAAAATCCTCATACACGTGATTTAATTCAAA
CATATCTGATGGGAATAATTGAGAAGCAATCAGATGGATCCTTTAATGTATATTCTGTTG
GTGATGTTGCTACAGGAATTAAAGATATTGAACGAAAAAACTTACATGATAAACTTATGC
CAAATACAGTTAACTATTGTGGAGGGACAATCATTGACTTTGAGAAAGGTAAAATTTTTC
TTGGTCAAAATAAAAATAAACCAGATGTCATCATTTTACCTCACAAGTCAATTGTTTTGC
AAGTTCGTGTATCTGAATTAGCTCCATCAAGTGATTTTTTCACTGAATACTCATTTAGAT
TTCCAAGAATTGATTCTATTAGATTTGATAAATGTTGGGATGAATCTTGTACTATGCAGC
AATTTCAACAAATGTGTAAGACTGGAAATAAAGTTGATGGACGAGTGGTTAAAGTTAATA
AACGAAATGTTGATGCTAAAGATATTCTTTCACCCGAGAAGAAACGTCGCATTGCATTTG
GAAAATCACGAGTAAGAGCAATCGAAAATTTTTGTCACGATTCACAAGAAGATGTTGAAC
CAATTGATGATGTACTAAATGGGATGGAATTTTGTGTTAAAACAACTTCTAAAAATTTAC
CATCAATAAATGATTTAAAATTACTTCTTAAAATACACGGCGCATCATTGACTGAATTTC
CCCGAAAGAAGAAAACTTTTGCAGTCATTGCTGGTGACATTGAACAACAAATTAAAATTT
ATATAAATGACAAGGTACATAACATATTGAAAGTCGATTGGTTGATTAAAAACTTTACAA
AACACTCGCCTCTACAGGATATTCCAAGACTCACGCCATTAGATTTTCATTTTATGACCG
ATGAAATGTACGAAGAAAAATTTAGGAAAGAGTATGACAAATATGGTGATTCTTATCATG
AGGTTCTTGAGACAGTTGATGAAATGATGAAAATAGTTAATAATATGCAGATTGAATTTG
ATATTTGTTCTCAAGAAATAAAAGAGCTACGACAAGAAATTTTTGATTTTAGTGGAACTG
AAAATTTTAAAATCTTTCAAGGGTACTATGCAAAATTTATCTATGGAGATGAGTTCAACA
TGACTATGAAGTGGAGTGAAAAAATCTTTGAGTTCTTAGGAGGTGTAATTATCAACAAAC
AAAATAGAAGGGATTTGTTAATTTTCGTCGATAAGGAAACATTTAATATTCGAATACATC
CAGAACTGAAAAACTTTCAAATTATTGATTATAAATTTATACTAAAATCTAATGATAATA
ACGCACTTGAAATATTAAACGATTACATGATAAAATAA
>g2448.t2 Gene=g2448 Length=717
MKLKISPAKILEKVHPLGGKLFTKYNHLSTVIEFIEKGQAIEAMKDVIKPFTPIRAMLSQ
KFSIDMNKMLEKFELYQEIKMDGERFQLHMENGEYKYFSRNAHDFSQCFNQFITPLIKYK
VVVHSVILDGEMIIWNKELRRFVTKGETDMDVKKMKDINHNMRPCFCAFDVLYLNGTSFI
DQPFYRRYEILHSLFDDRVGVLIKTNPVKIRDVEHLVSQFNKALDNNEEGIILKKADSTY
MPGERDKGGWYKMKADYFNDEVVEDFDCVIIGGYFKNPHTRDLIQTYLMGIIEKQSDGSF
NVYSVGDVATGIKDIERKNLHDKLMPNTVNYCGGTIIDFEKGKIFLGQNKNKPDVIILPH
KSIVLQVRVSELAPSSDFFTEYSFRFPRIDSIRFDKCWDESCTMQQFQQMCKTGNKVDGR
VVKVNKRNVDAKDILSPEKKRRIAFGKSRVRAIENFCHDSQEDVEPIDDVLNGMEFCVKT
TSKNLPSINDLKLLLKIHGASLTEFPRKKKTFAVIAGDIEQQIKIYINDKVHNILKVDWL
IKNFTKHSPLQDIPRLTPLDFHFMTDEMYEEKFRKEYDKYGDSYHEVLETVDEMMKIVNN
MQIEFDICSQEIKELRQEIFDFSGTENFKIFQGYYAKFIYGDEFNMTMKWSEKIFEFLGG
VIINKQNRRDLLIFVDKETFNIRIHPELKNFQIIDYKFILKSNDNNALEILNDYMIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2448.t2 | CDD | cd07903 | Adenylation_DNA_ligase_IV | 45 | 259 | 9.19082E-70 |
| 10 | g2448.t2 | Coils | Coil | Coil | 598 | 618 | - |
| 7 | g2448.t2 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 49 | 256 | 8.2E-53 |
| 9 | g2448.t2 | Gene3D | G3DSA:2.40.50.140 | - | 258 | 415 | 6.1E-30 |
| 8 | g2448.t2 | Gene3D | G3DSA:3.40.50.10190 | - | 477 | 604 | 9.3E-14 |
| 3 | g2448.t2 | PANTHER | PTHR45997:SF1 | DNA LIGASE 4 | 1 | 640 | 8.5E-116 |
| 4 | g2448.t2 | PANTHER | PTHR45997 | DNA LIGASE 4 | 1 | 640 | 8.5E-116 |
| 2 | g2448.t2 | Pfam | PF01068 | ATP dependent DNA ligase domain | 57 | 254 | 4.0E-44 |
| 1 | g2448.t2 | Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 281 | 396 | 3.0E-8 |
| 15 | g2448.t2 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 157 | 293 | 25.005 |
| 16 | g2448.t2 | ProSiteProfiles | PS50172 | BRCT domain profile. | 466 | 557 | 7.97 |
| 13 | g2448.t2 | SMART | SM00292 | BRCT_7 | 468 | 547 | 0.79 |
| 12 | g2448.t2 | SMART | SM00292 | BRCT_7 | 628 | 706 | 21.0 |
| 6 | g2448.t2 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 50 | 255 | 8.15E-41 |
| 5 | g2448.t2 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 263 | 412 | 5.82E-20 |
| 14 | g2448.t2 | TIGRFAM | TIGR00574 | dnl1: DNA ligase I, ATP-dependent (dnl1) | 12 | 411 | 9.9E-73 |
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.
