General information for g10966.t65
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.t65 | TTS | g10966.t65 | 13051260 | 13051260 |
| chr_1 | g10966 | g10966.t65 | isoform | g10966.t65 | 13052059 | 13054209 |
| chr_1 | g10966 | g10966.t65 | exon | g10966.t65.exon1 | 13052059 | 13053335 |
| chr_1 | g10966 | g10966.t65 | cds | g10966.t65.CDS1 | 13052060 | 13053335 |
| chr_1 | g10966 | g10966.t65 | exon | g10966.t65.exon2 | 13053389 | 13053685 |
| chr_1 | g10966 | g10966.t65 | cds | g10966.t65.CDS2 | 13053389 | 13053685 |
| chr_1 | g10966 | g10966.t65 | exon | g10966.t65.exon3 | 13053743 | 13054209 |
| chr_1 | g10966 | g10966.t65 | cds | g10966.t65.CDS3 | 13053743 | 13054032 |
| chr_1 | g10966 | g10966.t65 | TSS | g10966.t65 | 13054224 | 13054224 |
Sequences
>g10966.t65 Gene=g10966 Length=2041
ATGCAGAAATCAATTCTGTAAGAAATAAGGATTTTGATTTAATTTAAATAATACTTAATG
ATATTATGTTTTCAGCTCATTTTTTACTAAAAAGGAAACAAAAGAAAGTGATCAATCACA
AATAGAGCAACAGCAACCAATAGAAAAAGAAGAGGAGGAGAAAAAGTAAATAAAGTCATG
TTTGTATTTAGATCTCTTCTGAGAAATTACACGAATTTAACAAGAAATTCTGAGTCATTC
AATCAATTTCAAAGAAAATTAGTGCTTAACAATCTTTCTTTATTCTCAATTAGTTCGAGT
CCCGATAATTCACCAATTAAAACTGTTCCAAAGAAGAAACGCAAAATTGTTTCAAGTGAT
GAAGAAGAGACGCCTGTGGCCAAAAAGCAAGAAATCGAGAAGAAATCTTCACCAGCTGTT
ATAAAGAAGGAAGTACAGAAAAAATCATCACCAGCTGCTAAAAAACAAACGGTCAAAAAA
GAAACTACACCAAAATCTAAAACAACAATCAAGACAAAAGAAAAGACATCAGAAAAGAAA
GTTGTGGTTACTAAAATCAAAACTGAATCATCTCCAGAAGAAAATAAACCTGAAAATGGA
CAAGTTAAGATTGAAGTTGAAAGTTTTACCAAATCTACTTCGATAATAGATAGCAATGTG
TTGAAATTGCAAAGTGCTGGTTCTGGTCAGAAAGGTTCTGATTATAATCCAGGGAAGAAA
AATTATCATCCAATTAATGATGCATTCTGGAAAAAGGGTGAAAAAACACCGTATTTGGCT
ATTGCAAAAACATTCGAGATAATTGAAGAAAACAGCAGTCGATTAAGAATGATGGAAATT
TTGAGCAATTACTTTCGATCTGTTATTGTATTGAGTCCCAACGATTTGTTGCCAAGTATT
TATTTGTGTCTCAATCAAGTGGCACCTGCATTTGAAGGGTTAGAATTGGGAGTAGCAGAA
ACAAACATCATGAAAGCCATAGGTCAAACAACAGGTCGTAGTTTACAACAAATCAAGAGT
GATGCACAGCAGACTGGAGATCTTGGAATTGTTGCTGAAAGATCAAGAAGCAATCAAAGA
ATGATGTTCACTCCTGCACCACACACTGTCGAAGGAATGTTCAATAAGCTTAAAACAATC
GCTAAAATGAGTGGTGCAACATCAATGCAAAAAAAAGTTGATACCATTAAAGGAATTTTT
GTAGCATGTCGACATTCAGAAGCAAGATATTTTGTTCGCTCATTGCTTGGAAAATTGAGA
ATTGGTCTTGCCGAACAATCTTTGCTGCAGGCACTTGCTCAAGCTATAACTTTGACACCT
CCACAAGACAATAAAAACGAACCTTACAAATTGAATGCCTTAGAAAATCGTAATGAAGCA
ACAATCAAGCAAAAAATAGAAGAAAATGCTCTCAAAATTAAAACAGTTTATTGTCAATGT
CCTGATTACAATCAAATTATACCTATTTTAATTTCTGATGGTGTTGATGTTTTACCCGAA
AAATGCAAAATGACACCTGGAGTTCCTTTAAAACCTATGCTTGCACAACCAACGAAAGGA
GTTAGTGAAGTTCTTGAGAGATTCGATGGTATTGAATTTACAAGTGAATGGAAATACGAT
GGTGAACGTGCACAAATTCATATGAATGAGAAAGGTGTAATAAGCATTTATAGCAGAAAT
CAAGAGAACAATACATCCAAATATCCTGATATTATTTCAAGAATTGAGTTAACAACAAAA
GATAGAGTCAAATCATTCATTCTAGATTGTGAAGCAGTGGCATGGGATCAAGAAAAAAAA
CAAATTCTCCCCTTCCAAATTTTATCCACACGAAAACGTAAAGACGCAAATGAAGCAGAG
ATCAAGGTTCAAGTTTGTGTTTACATGTTTGATTTACTCTATTTAAATGGCGAATCACTT
GTTGAAAAGCCATTTATTAAAAGACGAGAATTGCTTTATGACAATTTCCAAGAAGTAGAA
GGAATATGGAAGTTTGCTACAAAATTAGATACAAGTGACATGAATGAACTACAAAACTTC
C
>g10966.t65 Gene=g10966 Length=621
MFVFRSLLRNYTNLTRNSESFNQFQRKLVLNNLSLFSISSSPDNSPIKTVPKKKRKIVSS
DEEETPVAKKQEIEKKSSPAVIKKEVQKKSSPAAKKQTVKKETTPKSKTTIKTKEKTSEK
KVVVTKIKTESSPEENKPENGQVKIEVESFTKSTSIIDSNVLKLQSAGSGQKGSDYNPGK
KNYHPINDAFWKKGEKTPYLAIAKTFEIIEENSSRLRMMEILSNYFRSVIVLSPNDLLPS
IYLCLNQVAPAFEGLELGVAETNIMKAIGQTTGRSLQQIKSDAQQTGDLGIVAERSRSNQ
RMMFTPAPHTVEGMFNKLKTIAKMSGATSMQKKVDTIKGIFVACRHSEARYFVRSLLGKL
RIGLAEQSLLQALAQAITLTPPQDNKNEPYKLNALENRNEATIKQKIEENALKIKTVYCQ
CPDYNQIIPILISDGVDVLPEKCKMTPGVPLKPMLAQPTKGVSEVLERFDGIEFTSEWKY
DGERAQIHMNEKGVISIYSRNQENNTSKYPDIISRIELTTKDRVKSFILDCEAVAWDQEK
KQILPFQILSTRKRKDANEAEIKVQVCVYMFDLLYLNGESLVEKPFIKRRELLYDNFQEV
EGIWKFATKLDTSDMNELQNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10966.t65 | CDD | cd07900 | Adenylation_DNA_ligase_I_Euk | 442 | 621 | 9.75623E-110 |
| 9 | g10966.t65 | Coils | Coil | Coil | 618 | 621 | - |
| 8 | g10966.t65 | Gene3D | G3DSA:1.10.3260.10 | - | 172 | 452 | 4.7E-113 |
| 7 | g10966.t65 | Gene3D | G3DSA:3.30.470.30 | DNA ligase/mRNA capping enzyme | 453 | 621 | 3.0E-53 |
| 12 | g10966.t65 | MobiDBLite | mobidb-lite | consensus disorder prediction | 42 | 115 | - |
| 13 | g10966.t65 | MobiDBLite | mobidb-lite | consensus disorder prediction | 48 | 115 | - |
| 3 | g10966.t65 | PANTHER | PTHR45674:SF4 | DNA LIGASE 1 | 49 | 621 | 1.0E-201 |
| 4 | g10966.t65 | PANTHER | PTHR45674 | DNA LIGASE 1/3 FAMILY MEMBER | 49 | 621 | 1.0E-201 |
| 1 | g10966.t65 | Pfam | PF04675 | DNA ligase N terminus | 198 | 374 | 1.7E-43 |
| 2 | g10966.t65 | Pfam | PF01068 | ATP dependent DNA ligase domain | 453 | 621 | 1.1E-50 |
| 11 | g10966.t65 | ProSitePatterns | PS00697 | ATP-dependent DNA ligase AMP-binding site. | 477 | 485 | - |
| 15 | g10966.t65 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 559 | 621 | 16.897 |
| 5 | g10966.t65 | SUPERFAMILY | SSF117018 | ATP-dependent DNA ligase DNA-binding domain | 175 | 444 | 2.62E-86 |
| 6 | g10966.t65 | SUPERFAMILY | SSF56091 | DNA ligase/mRNA capping enzyme, catalytic domain | 449 | 620 | 1.5E-40 |
| 14 | g10966.t65 | TIGRFAM | TIGR00574 | dnl1: DNA ligase I, ATP-dependent (dnl1) | 256 | 621 | 1.5E-99 |
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 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.
