General information for g10966.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA ligase 1.
Parent gene
- The parent gene g10966 is located on chr_1: 13052059..13054209 (- 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 | g10966 | g10966.t1 | TTS | g10966.t1 | 13051260 | 13051260 |
| chr_1 | g10966 | g10966.t1 | isoform | g10966.t1 | 13051436 | 13054209 |
| chr_1 | g10966 | g10966.t1 | exon | g10966.t1.exon1 | 13051436 | 13053335 |
| chr_1 | g10966 | g10966.t1 | cds | g10966.t1.CDS1 | 13051436 | 13053335 |
| chr_1 | g10966 | g10966.t1 | exon | g10966.t1.exon2 | 13053389 | 13053685 |
| chr_1 | g10966 | g10966.t1 | cds | g10966.t1.CDS2 | 13053389 | 13053685 |
| chr_1 | g10966 | g10966.t1 | exon | g10966.t1.exon3 | 13053743 | 13053916 |
| chr_1 | g10966 | g10966.t1 | cds | g10966.t1.CDS3 | 13053743 | 13053916 |
| chr_1 | g10966 | g10966.t1 | exon | g10966.t1.exon4 | 13054045 | 13054134 |
| chr_1 | g10966 | g10966.t1 | cds | g10966.t1.CDS4 | 13054045 | 13054134 |
| chr_1 | g10966 | g10966.t1 | exon | g10966.t1.exon5 | 13054193 | 13054209 |
| chr_1 | g10966 | g10966.t1 | cds | g10966.t1.CDS5 | 13054193 | 13054209 |
| chr_1 | g10966 | g10966.t1 | TSS | g10966.t1 | 13054224 | 13054224 |
Sequences
>g10966.t1 Gene=g10966 Length=2478
ATGCAGAAATCAATTCTCTCATTTTTTACTAAAAAGGAAACAAAAGAAAGTGATCAATCA
CAAATAGAGCAACAGCAACCAATAGAAAAAGAAGAGGAGGAGAAAAATTCGAGTCCCGAT
AATTCACCAATTAAAACTGTTCCAAAGAAGAAACGCAAAATTGTTTCAAGTGATGAAGAA
GAGACGCCTGTGGCCAAAAAGCAAGAAATCGAGAAGAAATCTTCACCAGCTGTTATAAAG
AAGGAAGTACAGAAAAAATCATCACCAGCTGCTAAAAAACAAACGGTCAAAAAAGAAACT
ACACCAAAATCTAAAACAACAATCAAGACAAAAGAAAAGACATCAGAAAAGAAAGTTGTG
GTTACTAAAATCAAAACTGAATCATCTCCAGAAGAAAATAAACCTGAAAATGGACAAGTT
AAGATTGAAGTTGAAAGTTTTACCAAATCTACTTCGATAATAGATAGCAATGTGTTGAAA
TTGCAAAGTGCTGGTTCTGGTCAGAAAGGTTCTGATTATAATCCAGGGAAGAAAAATTAT
CATCCAATTAATGATGCATTCTGGAAAAAGGGTGAAAAAACACCGTATTTGGCTATTGCA
AAAACATTCGAGATAATTGAAGAAAACAGCAGTCGATTAAGAATGATGGAAATTTTGAGC
AATTACTTTCGATCTGTTATTGTATTGAGTCCCAACGATTTGTTGCCAAGTATTTATTTG
TGTCTCAATCAAGTGGCACCTGCATTTGAAGGGTTAGAATTGGGAGTAGCAGAAACAAAC
ATCATGAAAGCCATAGGTCAAACAACAGGTCGTAGTTTACAACAAATCAAGAGTGATGCA
CAGCAGACTGGAGATCTTGGAATTGTTGCTGAAAGATCAAGAAGCAATCAAAGAATGATG
TTCACTCCTGCACCACACACTGTCGAAGGAATGTTCAATAAGCTTAAAACAATCGCTAAA
ATGAGTGGTGCAACATCAATGCAAAAAAAAGTTGATACCATTAAAGGAATTTTTGTAGCA
TGTCGACATTCAGAAGCAAGATATTTTGTTCGCTCATTGCTTGGAAAATTGAGAATTGGT
CTTGCCGAACAATCTTTGCTGCAGGCACTTGCTCAAGCTATAACTTTGACACCTCCACAA
GACAATAAAAACGAACCTTACAAATTGAATGCCTTAGAAAATCGTAATGAAGCAACAATC
AAGCAAAAAATAGAAGAAAATGCTCTCAAAATTAAAACAGTTTATTGTCAATGTCCTGAT
TACAATCAAATTATACCTATTTTAATTTCTGATGGTGTTGATGTTTTACCCGAAAAATGC
AAAATGACACCTGGAGTTCCTTTAAAACCTATGCTTGCACAACCAACGAAAGGAGTTAGT
GAAGTTCTTGAGAGATTCGATGGTATTGAATTTACAAGTGAATGGAAATACGATGGTGAA
CGTGCACAAATTCATATGAATGAGAAAGGTGTAATAAGCATTTATAGCAGAAATCAAGAG
AACAATACATCCAAATATCCTGATATTATTTCAAGAATTGAGTTAACAACAAAAGATAGA
GTCAAATCATTCATTCTAGATTGTGAAGCAGTGGCATGGGATCAAGAAAAAAAACAAATT
CTCCCCTTCCAAATTTTATCCACACGAAAACGTAAAGACGCAAATGAAGCAGAGATCAAG
GTTCAAGTTTGTGTTTACATGTTTGATTTACTCTATTTAAATGGCGAATCACTTGTTGAA
AAGCCATTTATTAAAAGACGAGAATTGCTTTATGACAATTTCCAAGAAGTAGAAGGAATA
TGGAAGTTTGCTACAAAATTAGATACAAGTGACATGAATGAACTACAAAACTTCCTAGAT
GAAGCAGTTAAAGGCAATTGCGAAGGACTGATGGTGAAAACTCTCGAGAAAGAAGCTACA
TATGAAATTGCTAAACGATCACGAAATTGGCTCAAACTTAAAAAAGATTACCTGTCAGGT
GTTGGCGATTCATTAGATTTAGTAGTTCTTGGTGGATATCGTGGAAAAGGCAAAAGAACT
GGTATGTTTGGTGGATTCTTACTTGGATGTTATGATCATGAAAATGAAGAATACCAGAGT
ATATGCAAAATTGGAACAGGTTTTAGTGATGAAGATTTGAAAACACATTCAGAATTTTTC
AAAGATCACATTATAAAAGAACCCCGTTCATATTATCAATCAGATTCTAGTCTTACGCCT
GACGATTGGTTTGATGCTGTTCAAGTTTGGGAAGTAAAATGTGCAGATTTATCATTATCA
CCCATTCATCGTGCTGCCATTGGTATTGTAGATCCTGAAAAGGGAATTTCTTTGCGTTTT
CCTCGCTTCATTCGTATTCGTGATGATAAAAAGGTTGAAGATGCCACATCGGCAAAACAA
GTTGCTGACATGTATCAGAATCAAGATCAAATTAAAAATCAGCAATCAACAAGAGACATC
GAAGAAGATTTTTATTGA
>g10966.t1 Gene=g10966 Length=825
MQKSILSFFTKKETKESDQSQIEQQQPIEKEEEEKNSSPDNSPIKTVPKKKRKIVSSDEE
ETPVAKKQEIEKKSSPAVIKKEVQKKSSPAAKKQTVKKETTPKSKTTIKTKEKTSEKKVV
VTKIKTESSPEENKPENGQVKIEVESFTKSTSIIDSNVLKLQSAGSGQKGSDYNPGKKNY
HPINDAFWKKGEKTPYLAIAKTFEIIEENSSRLRMMEILSNYFRSVIVLSPNDLLPSIYL
CLNQVAPAFEGLELGVAETNIMKAIGQTTGRSLQQIKSDAQQTGDLGIVAERSRSNQRMM
FTPAPHTVEGMFNKLKTIAKMSGATSMQKKVDTIKGIFVACRHSEARYFVRSLLGKLRIG
LAEQSLLQALAQAITLTPPQDNKNEPYKLNALENRNEATIKQKIEENALKIKTVYCQCPD
YNQIIPILISDGVDVLPEKCKMTPGVPLKPMLAQPTKGVSEVLERFDGIEFTSEWKYDGE
RAQIHMNEKGVISIYSRNQENNTSKYPDIISRIELTTKDRVKSFILDCEAVAWDQEKKQI
LPFQILSTRKRKDANEAEIKVQVCVYMFDLLYLNGESLVEKPFIKRRELLYDNFQEVEGI
WKFATKLDTSDMNELQNFLDEAVKGNCEGLMVKTLEKEATYEIAKRSRNWLKLKKDYLSG
VGDSLDLVVLGGYRGKGKRTGMFGGFLLGCYDHENEEYQSICKIGTGFSDEDLKTHSEFF
KDHIIKEPRSYYQSDSSLTPDDWFDAVQVWEVKCADLSLSPIHRAAIGIVDPEKGISLRF
PRFIRIRDDKKVEDATSAKQVADMYQNQDQIKNQQSTRDIEEDFY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g10966.t1 | CDD | cd07900 | Adenylation_DNA_ligase_I_Euk | 439 | 657 | 4.94632E-142 |
| 14 | g10966.t1 | CDD | cd07969 | OBF_DNA_ligase_I | 662 | 807 | 4.20773E-93 |
| 10 | g10966.t1 | Gene3D | G3DSA:1.10.3260.10 | - | 169 | 452 | 8.7E-113 |
| 12 | g10966.t1 | Gene3D | G3DSA:3.30.1490.70 | - | 460 | 658 | 3.3E-75 |
| 9 | g10966.t1 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 479 | 604 | 3.3E-75 |
| 11 | g10966.t1 | Gene3D | G3DSA:2.40.50.140 | - | 663 | 809 | 2.7E-61 |
| 17 | g10966.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 114 | - |
| 18 | g10966.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 114 | - |
| 19 | g10966.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 805 | 825 | - |
| 4 | g10966.t1 | PANTHER | PTHR45674:SF4 | DNA LIGASE 1 | 12 | 824 | 0.0 |
| 5 | g10966.t1 | PANTHER | PTHR45674 | DNA LIGASE 1/3 FAMILY MEMBER | 12 | 824 | 0.0 |
| 1 | g10966.t1 | Pfam | PF04675 | DNA ligase N terminus | 195 | 371 | 2.9E-43 |
| 3 | g10966.t1 | Pfam | PF01068 | ATP dependent DNA ligase domain | 450 | 654 | 1.2E-65 |
| 2 | g10966.t1 | Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 679 | 790 | 7.3E-24 |
| 16 | g10966.t1 | ProSitePatterns | PS00697 | ATP-dependent DNA ligase AMP-binding site. | 474 | 482 | - |
| 15 | g10966.t1 | ProSitePatterns | PS00333 | ATP-dependent DNA ligase signature 2. | 628 | 654 | - |
| 21 | g10966.t1 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 556 | 692 | 46.168 |
| 7 | g10966.t1 | SUPERFAMILY | SSF117018 | ATP-dependent DNA ligase DNA-binding domain | 172 | 441 | 4.84E-86 |
| 8 | g10966.t1 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 443 | 660 | 4.03E-54 |
| 6 | g10966.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 662 | 808 | 1.76E-49 |
| 20 | g10966.t1 | TIGRFAM | TIGR00574 | dnl1: DNA ligase I, ATP-dependent (dnl1) | 253 | 806 | 4.5E-175 |
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:0003910 | DNA ligase (ATP) activity | MF |
| GO:0003909 | DNA ligase activity | MF |
| GO:0006310 | DNA recombination | BP |
KEGG
Orthology
- This transcript has been annotated with K10747 (DNA ligase 1)
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.
