General information for g817.t42
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ribonuclease H1.
Parent gene
- The parent gene g817 is located on chr_3: 6162517..6163196 (- 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 | g817 | g817.t42 | TTS | g817.t42 | 6162068 | 6162068 |
| chr_3 | g817 | g817.t42 | isoform | g817.t42 | 6162120 | 6163196 |
| chr_3 | g817 | g817.t42 | exon | g817.t42.exon1 | 6162120 | 6162549 |
| chr_3 | g817 | g817.t42 | cds | g817.t42.CDS1 | 6162120 | 6162549 |
| chr_3 | g817 | g817.t42 | exon | g817.t42.exon2 | 6162609 | 6163004 |
| chr_3 | g817 | g817.t42 | cds | g817.t42.CDS2 | 6162609 | 6163003 |
| chr_3 | g817 | g817.t42 | exon | g817.t42.exon3 | 6163071 | 6163196 |
| chr_3 | g817 | g817.t42 | TSS | g817.t42 | NA | NA |
Sequences
>g817.t42 Gene=g817 Length=952
TCAATTATTACACCATTAAATTATTAATAATGCTTCTTAATATCTTACTTTTTAATTTTA
TAATTCAATTTTGAATAATTAAAGAGAAATTCTATAAAAATAATTCATCATCAGAATTTC
CTACACAATGCCTTTCTATGCAGTAGCAAAAGGCAAGGAAACTGGGATATATAGCACTTG
GGATGACTGTCAGCTGCAAGTGAAAGGTTTCAGTGGTGCAATTTATAAGAAATTTAAAAC
AAAAGCAGAAGCTGAAGAATTTATCGAAAAGAAATCTGAACCAGTAAAAAAGAAACGCAA
AATAGAATACACCGAAGAGGATGAGATTCGTGACATATTAAAATTCGTAGAAACGTGTGA
AGATGAAGAAATTCCAACATCATCAACAAATAAATCGACAAACAAGGATTACAGTAAACC
CAAAATAAAAAGTGAACTTCCAGGAGAGACTACTCTAAAGAAATATGGCAAATATATATT
TAATGAAGATGCTAATGGCTTTGTTCATGTGTTTACAGATGGTTCGTGTGAAAGTAATGG
ATCAAAGTTTGCACGTGCAGGTTTAGGCGTATATTTTGGTAAAAATCATCCACTTAATGC
AAGTGAACCAGTTAAAGGAAAAGCAACAAACAATGTAGGAGAAATTCAAGCTTCAATAAA
AGCTATTGAGTCAGCACAAAGTTGTGAAATACGAAAACTTAACATTTTCACTGATTCACA
ATACCTTATGAATTCAATTTGCATTTGGATGCCAAAATGGAAGAAAAATAAGTGGATGTT
AGCTAATCAAAAAGAAGTAAAGAATAAGATAGATTTTCAAAGATTAGATCAATTGATAAA
CTCTGGTAATATGCTTATTAAATGGTCATATATACCTGCTCATAAAGGACATGATGGGAA
TGAAGCAGCTGATAGACTTGCAAAAGAAGGTGCTCAACGTTATAAATTTTAA
>g817.t42 Gene=g817 Length=274
MPFYAVAKGKETGIYSTWDDCQLQVKGFSGAIYKKFKTKAEAEEFIEKKSEPVKKKRKIE
YTEEDEIRDILKFVETCEDEEIPTSSTNKSTNKDYSKPKIKSELPGETTLKKYGKYIFNE
DANGFVHVFTDGSCESNGSKFARAGLGVYFGKNHPLNASEPVKGKATNNVGEIQASIKAI
ESAQSCEIRKLNIFTDSQYLMNSICIWMPKWKKNKWMLANQKEVKNKIDFQRLDQLINSG
NMLIKWSYIPAHKGHDGNEAADRLAKEGAQRYKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g817.t42 | CDD | cd09280 | RNase_HI_eukaryote_like | 127 | 270 | 0.000 |
| 7 | g817.t42 | Gene3D | G3DSA:3.40.970.10 | Ribonuclease Hi; Chain A | 1 | 50 | 0.000 |
| 8 | g817.t42 | Gene3D | G3DSA:3.30.420.10 | - | 121 | 272 | 0.000 |
| 3 | g817.t42 | PANTHER | PTHR10642 | RIBONUCLEASE H1 | 1 | 272 | 0.000 |
| 4 | g817.t42 | PANTHER | PTHR10642:SF23 | RIBONUCLEASE H1 | 1 | 272 | 0.000 |
| 10 | g817.t42 | PIRSF | PIRSF036852 | RNase_H1_euk | 1 | 274 | 0.000 |
| 1 | g817.t42 | Pfam | PF01693 | Caulimovirus viroplasmin | 3 | 45 | 0.000 |
| 2 | g817.t42 | Pfam | PF00075 | RNase H | 126 | 269 | 0.000 |
| 9 | g817.t42 | ProSiteProfiles | PS50879 | RNase H domain profile. | 122 | 270 | 24.329 |
| 6 | g817.t42 | SUPERFAMILY | SSF55658 | L9 N-domain-like | 2 | 46 | 0.000 |
| 5 | g817.t42 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 124 | 271 | 0.000 |
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:0000287 | magnesium ion binding | MF |
| GO:0004523 | RNA-DNA hybrid ribonuclease activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03469 (ribonuclease HI)
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.
