General information for g8268.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribonuclease H2 subunit A.
Parent gene
- The parent gene g8268 is located on chr_2: 29416572..29417489 (+ 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_2 | g8268 | g8268.t4 | TSS | g8268.t4 | 29415446 | 29415446 |
| chr_2 | g8268 | g8268.t4 | isoform | g8268.t4 | 29415497 | 29416572 |
| chr_2 | g8268 | g8268.t4 | exon | g8268.t4.exon1 | 29415497 | 29415629 |
| chr_2 | g8268 | g8268.t4 | exon | g8268.t4.exon2 | 29415748 | 29416572 |
| chr_2 | g8268 | g8268.t4 | cds | g8268.t4.CDS1 | 29415784 | 29416572 |
| chr_2 | g8268 | g8268.t4 | TTS | g8268.t4 | 29416615 | 29416615 |
Sequences
>g8268.t4 Gene=g8268 Length=958
ATGGACTCATTAAATACAATAAAATGTTTAGAATCTCTTAAAAATTATATTAAAAGACAG
GATAATTCAAAGAGTTTTGTGTACTTTTCGTCAATTCCAGACATTTGCAAAACAGAAAAA
TGTATTTTAGGAGATTATTAATTTTTTGTAATTATCAGTTTTAGGGCCTATGGTCTACGG
AATCGCTTTTTGTCCTAAATCCAATGAATCAATCCTTAAAGATTTGGGATGTGCAGATTC
TAAGCAACTTAATGAACAACAAAGAGATGATATCTTTGTCAATACTAATCAAAAAGATTA
TTCTACTGAATCAATTGGTTGGGCTACTAATGTCATTTCTCCTAATGAAATAAGTACCAG
TATGTTAAGACGAACAAAAAGAAGTTTAAATGAAGTTTCTATGGATAGCGCAATATCATT
AATTAAAACAGCTATTGAAAATGGAGTGAATGTTGCAGAAATCTTTGTCGATACAGTTGG
CCCTCCAGAAAAATATCAAGCAAAATTAAAAGCTATTTTTCCATCATGTAAAGTTACGGT
CGCTAAGAAAGCTGATTCAACTTATCCAATTGTATCTCTGGCTTCAATTTGTGCTAAAGT
CTCACGTGATCATGCACTTAAAGTATGGGAATTTAGAGAAAACGTAGAAGTGCCTGAAGA
TGGCTTTGGTTCAGGATACCCAGGAGACCCTGTAACAAAAAGATTTTTACGTAATTTTGA
GCCTCTTTTTGGGTATTCACGTATTGTTAGATTCAGTTGGTCGACTGCTTCAAATCAATT
GGAAGAGAATAATGCTGTAACAATCGAATTTGAGGAAGAAGAGGAGGGAAGCGAGAAGAA
AGTAAAATTAGCCAGTAAAAAGATGACTGCATTTTTCAAATCTGAAGTTCCTGTAAAAAA
ATTCAAGCGACACAATTTTTTTAAAGAAAGATTTTTAGAGGATGTAATTGATTTTTAA
>g8268.t4 Gene=g8268 Length=262
MVYGIAFCPKSNESILKDLGCADSKQLNEQQRDDIFVNTNQKDYSTESIGWATNVISPNE
ISTSMLRRTKRSLNEVSMDSAISLIKTAIENGVNVAEIFVDTVGPPEKYQAKLKAIFPSC
KVTVAKKADSTYPIVSLASICAKVSRDHALKVWEFRENVEVPEDGFGSGYPGDPVTKRFL
RNFEPLFGYSRIVRFSWSTASNQLEENNAVTIEFEEEEEGSEKKVKLASKKMTAFFKSEV
PVKKFKRHNFFKERFLEDVIDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8268.t4 | CDD | cd07181 | RNase_HII_eukaryota_like | 1 | 209 | 0 |
| 6 | g8268.t4 | Gene3D | G3DSA:3.30.420.10 | - | 1 | 161 | 0 |
| 5 | g8268.t4 | Gene3D | G3DSA:1.10.10.460 | Ribonuclease hii. Domain 2 | 162 | 208 | 0 |
| 2 | g8268.t4 | PANTHER | PTHR10954 | RIBONUCLEASE H2 SUBUNIT A | 1 | 241 | 0 |
| 3 | g8268.t4 | PANTHER | PTHR10954:SF7 | RIBONUCLEASE H2 SUBUNIT A | 1 | 241 | 0 |
| 1 | g8268.t4 | Pfam | PF01351 | Ribonuclease HII | 1 | 199 | 0 |
| 4 | g8268.t4 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 1 | 205 | 0 |
| 7 | g8268.t4 | TIGRFAM | TIGR00729 | TIGR00729: ribonuclease HII | 1 | 203 | 0 |
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:0016070 | RNA metabolic process | BP |
| GO:0003723 | RNA binding | MF |
| GO:0004523 | RNA-DNA hybrid ribonuclease activity | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K10743 (ribonuclease H2 subunit A)
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.
