General information for g13423.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA ligase 3.
Parent gene
- The parent gene g13423 is located on chr_1: 29978606..29981262 (+ 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_1 | g13423 | g13423.t1 | TSS | g13423.t1 | 29978594 | 29978594 |
| chr_1 | g13423 | g13423.t1 | isoform | g13423.t1 | 29978606 | 29981262 |
| chr_1 | g13423 | g13423.t1 | exon | g13423.t1.exon1 | 29978606 | 29978701 |
| chr_1 | g13423 | g13423.t1 | cds | g13423.t1.CDS1 | 29978606 | 29978701 |
| chr_1 | g13423 | g13423.t1 | exon | g13423.t1.exon2 | 29978761 | 29981262 |
| chr_1 | g13423 | g13423.t1 | cds | g13423.t1.CDS2 | 29978761 | 29981262 |
| chr_1 | g13423 | g13423.t1 | TTS | g13423.t1 | 29981340 | 29981340 |
Sequences
>g13423.t1 Gene=g13423 Length=2598
ATGAGTGATAATGAGGACGTTGTTTTTAAGCAATTTGAAGTAGAGAGAGCAAAACAAGGT
CGAGCAAAATGCAAAAAGTGCAAAGAACCTTGCAAAGCTGGTGAATTAAGATTTGCTATT
TTAAATAAAAACAATCCATTTGGTGATGGTCCATTGAAAAATTGGTTTCATATAAAATGT
TTTTGTGAATCAAAAGCAAACAAGACGAAAATTGAACAAGCAACAACAAATGACATCAAT
GGCTGGGACTTATTAAATGATGATGACGTAAAAACTGTACTTAAACATATACCGATAACG
GTAGCAGCGACTCAGGAAAGTACATCAAAAAAGAGTAGCTCTTCTTCTTCTTCAACTGCC
ACCACTACCAAAGATAATCTTTTAAGTCAATTCAATTGGCTTGTTGAAAAAATAGCTAAT
GAGCCTAGTTATAACAATAAAAGTGCTATTATTAAAAAATATTTAAACGAAGGAAGTAAT
AAGAAAAAGTTTGAGGGTAATCAAGAGCTGTGGTTAAAATTATTAATACCTAAAGTTGAC
CAAAGAGTGTATAACTTGCAAGACAAACAGATCGTTAAACTGTTCTCAAAACTCTTTAAT
CTAAACCAAGAAGATTTACAACAAGACTTGTATGCCGGTGACGTCTCTGAAACTGTTGCA
AAATTTTTCAAAAAATCAAAAGCAATTAAACCCGTTGATGAAAGTAAATTAACATTGATG
GATGTTGATAAATTTTTAAATGAACTTGAATCTAGAACGAAAGAAGATGAGCAACAAAAA
CATTTTGAGGCATTTTGCAAAAAATGTACAACAAATGATATAAGAACTTTAATTAGACTA
ATTAAAAAGGATTTAAAAATGAATTGTCGTGAAAGGCATGTACTTGACTCATTACATGCA
GACGCTTATGAATGTTTCCAAAAGTCACGCGATCTTAAATTAATCATTGAACAATATGGA
AACGGAAATTCTAGTGCATCAAAAAGTTCTACTAAAATGGGTTTTAAAGTCATGACTGCA
GTTTCACCAATGTTAGCAGAACCATGCAAAAATTTTGATAAAGCATTGAAAAAATGTCCA
GAAGGGTTTTATAGTGAAATCAAATATGATGGTGAACGCGTGCAAATACACAAGCATGGA
AAAGATTTTAAGTTCTTTAGTCGAAATCTCAAACCAGTAATGGAGCATAAAATAGCAAAA
ATCAAAGATTATTTGCCAAAAGCATTCCCTAACGCAGATGATTTGATTCTTGATTCTGAG
ATTATCATGGTAGATACAACGAATGGAAATTTGCTGCCATTTGGTACTCTTGGCAAACAC
AAGAAAGAAGAACATAAAAATGCTTCAGCATGCTTGTACATCTTTGATTGTCTTTATTTC
AATGGTGAAGATTTGACAAAGAAAAAATTGAAAGAGCGTAGAAAATTTTTAGAGACGAAT
ATCAAACCAATTAAGTATCATATAGAATTATCAGAATATAAATTATTGAGGAAGAAAAAT
GAACTCATTGATATGACTAAAGAAGTGCTTAAAAAAGGTTTAGAAGGACTCGTACTCAAA
GGACTTGACACAGTTTACGAGCCAGGGAAACGTCGTTGGTTAAAAGTAAAGAAAGATTAC
TTGCTAGAAGGAAAAATTGCAGATTCTTGTGATTTGGTTGTACTCGGTGCATGGTATGGA
ACTGGAAAAATGGGTAGTCGATTTTCAATTTATTTGATGGGATGTCATGATGAAAAATTA
AAAATATGGAAAACAGTAACAAAAGTTCATAGTGGATTAGATGACATGACTATTGAACGT
ATGCATAAACAACTGACTCCTCTAGTTGAACCTTGGAATGTTAATAAAAAGCTTCCAGAT
TGGGTAAGGATTGATAGAACATTAATTCCCGATGTCCTTGCAAAAGATCCATTTGCAATG
CCAGTGTTTGAGGTTGTTGCTGCTGAGTTTACAAACAGCGATGTTCATACAAGCAATTCA
ATTTCAATGAGATTCCCACGTATTACAAAAATACGAGAAGATAAATCACCAAGAGAAGCG
ACAACATTAGATGAATTGACTCATCTCTATGAAGAATCTAAATCAGGGATAAATATTGAT
GAACTTAATAAGTTAAAAAGCAATAGTCAATCTGATGATGCAAGTGAAGCAAAATCGACT
TTCATAAAAAAAGATTTGTCATCATCGTCTATGGGCGCAATGAAGCGAAAGGCTGATATG
AAAAATGCAAGCAATAATAAAGAACATGACGACAGCAATGAGTCGACACCTATAAAGAAA
GTAAAAAGTAACAGTACGGAGATGGAAGAAAAAATTGTTGAAAGTGATATTTTCAAGGGC
TTCATACTGTTTGATAACAAGTGCGTGTCAAATGAATTGAATGATTTTAGAAAACATGGA
GGGAAAATAACAAAAATATCAAAAGAAGCAAATCTTGTGATTCACGATTCATCAGAAATT
AAGGATGATTTGGAAAATTTGAGAAAGCAATTCACTCCCACATGTCGGCATTATCAAAAA
TCTTGGCTAATTGAGTGTCTAGAGACGAAGAAAATCGCAAATGGTCTTAATCACTTTGTT
AAATTACGTCAAAAATAA
>g13423.t1 Gene=g13423 Length=865
MSDNEDVVFKQFEVERAKQGRAKCKKCKEPCKAGELRFAILNKNNPFGDGPLKNWFHIKC
FCESKANKTKIEQATTNDINGWDLLNDDDVKTVLKHIPITVAATQESTSKKSSSSSSSTA
TTTKDNLLSQFNWLVEKIANEPSYNNKSAIIKKYLNEGSNKKKFEGNQELWLKLLIPKVD
QRVYNLQDKQIVKLFSKLFNLNQEDLQQDLYAGDVSETVAKFFKKSKAIKPVDESKLTLM
DVDKFLNELESRTKEDEQQKHFEAFCKKCTTNDIRTLIRLIKKDLKMNCRERHVLDSLHA
DAYECFQKSRDLKLIIEQYGNGNSSASKSSTKMGFKVMTAVSPMLAEPCKNFDKALKKCP
EGFYSEIKYDGERVQIHKHGKDFKFFSRNLKPVMEHKIAKIKDYLPKAFPNADDLILDSE
IIMVDTTNGNLLPFGTLGKHKKEEHKNASACLYIFDCLYFNGEDLTKKKLKERRKFLETN
IKPIKYHIELSEYKLLRKKNELIDMTKEVLKKGLEGLVLKGLDTVYEPGKRRWLKVKKDY
LLEGKIADSCDLVVLGAWYGTGKMGSRFSIYLMGCHDEKLKIWKTVTKVHSGLDDMTIER
MHKQLTPLVEPWNVNKKLPDWVRIDRTLIPDVLAKDPFAMPVFEVVAAEFTNSDVHTSNS
ISMRFPRITKIREDKSPREATTLDELTHLYEESKSGINIDELNKLKSNSQSDDASEAKST
FIKKDLSSSSMGAMKRKADMKNASNNKEHDDSNESTPIKKVKSNSTEMEEKIVESDIFKG
FILFDNKCVSNELNDFRKHGGKITKISKEANLVIHDSSEIKDDLENLRKQFTPTCRHYQK
SWLIECLETKKIANGLNHFVKLRQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g13423.t1 | CDD | cd07902 | Adenylation_DNA_ligase_III | 328 | 540 | 1.6208E-115 |
| 13 | g13423.t1 | Gene3D | G3DSA:3.30.1740.10 | - | 3 | 122 | 5.0E-23 |
| 15 | g13423.t1 | Gene3D | G3DSA:1.10.3260.10 | - | 123 | 324 | 1.6E-54 |
| 17 | g13423.t1 | Gene3D | G3DSA:3.30.1490.70 | - | 344 | 537 | 8.2E-74 |
| 14 | g13423.t1 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 372 | 491 | 8.2E-74 |
| 16 | g13423.t1 | Gene3D | G3DSA:2.40.50.140 | - | 548 | 694 | 8.0E-40 |
| 22 | g13423.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 728 | 764 | - |
| 23 | g13423.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 740 | 764 | - |
| 5 | g13423.t1 | PANTHER | PTHR45674 | DNA LIGASE 1/3 FAMILY MEMBER | 8 | 100 | 2.6E-219 |
| 7 | g13423.t1 | PANTHER | PTHR45674:SF9 | DNA LIGASE 3 | 8 | 100 | 2.6E-219 |
| 6 | g13423.t1 | PANTHER | PTHR45674 | DNA LIGASE 1/3 FAMILY MEMBER | 107 | 718 | 2.6E-219 |
| 8 | g13423.t1 | PANTHER | PTHR45674:SF9 | DNA LIGASE 3 | 107 | 718 | 2.6E-219 |
| 1 | g13423.t1 | Pfam | PF00645 | Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region | 15 | 97 | 6.9E-16 |
| 2 | g13423.t1 | Pfam | PF04675 | DNA ligase N terminus | 131 | 299 | 2.4E-31 |
| 4 | g13423.t1 | Pfam | PF01068 | ATP dependent DNA ligase domain | 343 | 537 | 2.0E-59 |
| 3 | g13423.t1 | Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 565 | 675 | 2.5E-15 |
| 20 | g13423.t1 | ProSitePatterns | PS00697 | ATP-dependent DNA ligase AMP-binding site. | 366 | 374 | - |
| 19 | g13423.t1 | ProSitePatterns | PS00333 | ATP-dependent DNA ligase signature 2. | 515 | 537 | - |
| 27 | g13423.t1 | ProSiteProfiles | PS50064 | Poly(ADP-ribose) polymerase zinc finger domain profile. | 12 | 98 | 22.827 |
| 25 | g13423.t1 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 443 | 577 | 39.202 |
| 26 | g13423.t1 | ProSiteProfiles | PS50172 | BRCT domain profile. | 773 | 860 | 10.808 |
| 21 | g13423.t1 | SMART | SM01336 | zf_PARP_3 | 15 | 98 | 9.1E-23 |
| 9 | g13423.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 10 | 99 | 4.28E-18 |
| 11 | g13423.t1 | SUPERFAMILY | SSF117018 | ATP-dependent DNA ligase DNA-binding domain | 171 | 300 | 9.42E-6 |
| 12 | g13423.t1 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 298 | 538 | 6.72E-48 |
| 10 | g13423.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 548 | 692 | 5.65E-33 |
| 24 | g13423.t1 | TIGRFAM | TIGR00574 | dnl1: DNA ligase I, ATP-dependent (dnl1) | 184 | 691 | 1.9E-133 |
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:0003910 | DNA ligase (ATP) activity | MF |
| GO:0071897 | DNA biosynthetic process | BP |
| GO:0003909 | DNA ligase activity | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0006310 | DNA recombination | BP |
KEGG
Orthology
- This transcript has been annotated with K10776 (DNA ligase 3)
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.
