General information for g10966.t64
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.t64 | TTS | g10966.t64 | 13051260 | 13051260 |
| chr_1 | g10966 | g10966.t64 | isoform | g10966.t64 | 13051436 | 13052059 |
| chr_1 | g10966 | g10966.t64 | exon | g10966.t64.exon1 | 13051436 | 13052059 |
| chr_1 | g10966 | g10966.t64 | cds | g10966.t64.CDS1 | 13051436 | 13052023 |
| chr_1 | g10966 | g10966.t64 | TSS | g10966.t64 | 13052220 | 13052220 |
Sequences
>g10966.t64 Gene=g10966 Length=624
CTAGATGAAGCAGTTAAAGGCAATTGCGAAGGACTGATGGTGAAAACTCTCGAGAAAGAA
GCTACATATGAAATTGCTAAACGATCACGAAATTGGCTCAAACTTAAAAAAGATTACCTG
TCAGGTGTTGGCGATTCATTAGATTTAGTAGTTCTTGGTGGATATCGTGGAAAAGGCAAA
AGAACTGGTATGTTTGGTGGATTCTTACTTGGATGTTATGATCATGAAAATGAAGAATAC
CAGAGTATATGCAAAATTGGAACAGGTTTTAGTGATGAAGATTTGAAAACACATTCAGAA
TTTTTCAAAGATCACATTATAAAAGAACCCCGTTCATATTATCAATCAGATTCTAGTCTT
ACGCCTGACGATTGGTTTGATGCTGTTCAAGTTTGGGAAGTAAAATGTGCAGATTTATCA
TTATCACCCATTCATCGTGCTGCCATTGGTATTGTAGATCCTGAAAAGGGAATTTCTTTG
CGTTTTCCTCGCTTCATTCGTATTCGTGATGATAAAAAGGTTGAAGATGCCACATCGGCA
AAACAAGTTGCTGACATGTATCAGAATCAAGATCAAATTAAAAATCAGCAATCAACAAGA
GACATCGAAGAAGATTTTTATTGA
>g10966.t64 Gene=g10966 Length=195
MVKTLEKEATYEIAKRSRNWLKLKKDYLSGVGDSLDLVVLGGYRGKGKRTGMFGGFLLGC
YDHENEEYQSICKIGTGFSDEDLKTHSEFFKDHIIKEPRSYYQSDSSLTPDDWFDAVQVW
EVKCADLSLSPIHRAAIGIVDPEKGISLRFPRFIRIRDDKKVEDATSAKQVADMYQNQDQ
IKNQQSTRDIEEDFY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10966.t64 | CDD | cd07969 | OBF_DNA_ligase_I | 32 | 177 | 1.05039E-97 |
| 7 | g10966.t64 | Gene3D | G3DSA:3.30.1490.70 | - | 1 | 32 | 1.3E-11 |
| 6 | g10966.t64 | Gene3D | G3DSA:2.40.50.140 | - | 33 | 179 | 1.1E-62 |
| 5 | g10966.t64 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 195 | - |
| 2 | g10966.t64 | PANTHER | PTHR45674:SF4 | DNA LIGASE 1 | 1 | 194 | 1.1E-106 |
| 3 | g10966.t64 | PANTHER | PTHR45674 | DNA LIGASE 1/3 FAMILY MEMBER | 1 | 194 | 1.1E-106 |
| 1 | g10966.t64 | Pfam | PF04679 | ATP dependent DNA ligase C terminal region | 49 | 160 | 4.3E-25 |
| 8 | g10966.t64 | ProSiteProfiles | PS50160 | ATP-dependent DNA ligase family profile. | 1 | 62 | 25.409 |
| 4 | g10966.t64 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 32 | 178 | 6.85E-51 |
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:0006281 | DNA repair | BP |
| GO:0005524 | ATP binding | MF |
| GO:0003910 | DNA ligase (ATP) 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.
