General information for g12060.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Ribonuclease H2 subunit B.
Parent gene
- The parent gene g12060 is located on chr_1: 20694034..20697136 (- 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 | g12060 | g12060.t1 | TTS | g12060.t1 | 20693040 | 20693040 |
| chr_1 | g12060 | g12060.t1 | isoform | g12060.t1 | 20693099 | 20694034 |
| chr_1 | g12060 | g12060.t1 | exon | g12060.t1.exon1 | 20693099 | 20693901 |
| chr_1 | g12060 | g12060.t1 | cds | g12060.t1.CDS1 | 20693099 | 20693901 |
| chr_1 | g12060 | g12060.t1 | exon | g12060.t1.exon2 | 20693962 | 20694034 |
| chr_1 | g12060 | g12060.t1 | cds | g12060.t1.CDS2 | 20693962 | 20694034 |
| chr_1 | g12060 | g12060.t1 | TSS | g12060.t1 | 20694064 | 20694064 |
Sequences
>g12060.t1 Gene=g12060 Length=876
ATGGCAAGAAGCAAAAAATCTGATATATCAAAATGTATTGAAAATAATACGACCAAAGTA
TTTTTTTTAGATAAGAATTTAATAAAAGAAAATATAGAAATTTTTAAAATACAACTACCA
AGAAAAACTTCTCTTTTCATAAAATCGTCTGAAGGAATTTATGAATTGTTGCAATTTAAT
GAAAAACATAGATGCTTTTTTATTGAAAATACTGTTTGTAGTAATGGAAAAATCTATGTT
GCAACCAAATTTGATCCTCTTTATGCTTTTATTCAATTACTTGAGGTAAATTGCAAAAAT
CGTGCACAACCAATAGATCAACTGCTTGAAAATAAGACAATAATATTCTCAGACTTTTTG
AAAATGAGTCAAATGAGGCTTATAGCCGACCAAAAAGGGTCAGACAATTTAAAAGCATTT
ATCTTCAATGAAGAGAAGGTATTAAAATGGCTAAAAATCAAATTTGCTAGAATACAAGAA
TCACTCAAGCAGCAAAAGATCATTTTTAGCGGATCATCGTCTCTTAATTTTGTTCAGTCA
ACATTAAATAACGATCAAATAGAAAATGATGATGAGATTGCTGCTACAGCATTAGGCATA
ATTTCAGAATACATTTCGCTTGACCTTTATGAGAAACTTGATGCATTTTATGGTATTAGC
GAAAAGTCAAAAGAACCTATCTCGCAAAAACGAAAGTCTGGTGTAAATGAAAAAGAGCCA
GACAGTAAGAAAATCAAGACAGAGGACGATGATGAAATAACAAAGGAAAATAAAAAGTCC
CAAATCACATCTAAAAGTGTCTCAAAAAATGTTGCAAAACTCGAAAAAGCTGCAAAAGGT
ACAAAATCAATAAGCTCTTTCTTTGCTAAAAAGTAG
>g12060.t1 Gene=g12060 Length=291
MARSKKSDISKCIENNTTKVFFLDKNLIKENIEIFKIQLPRKTSLFIKSSEGIYELLQFN
EKHRCFFIENTVCSNGKIYVATKFDPLYAFIQLLEVNCKNRAQPIDQLLENKTIIFSDFL
KMSQMRLIADQKGSDNLKAFIFNEEKVLKWLKIKFARIQESLKQQKIIFSGSSSLNFVQS
TLNNDQIENDDEIAATALGIISEYISLDLYEKLDAFYGISEKSKEPISQKRKSGVNEKEP
DSKKIKTEDDDEITKENKKSQITSKSVSKNVAKLEKAAKGTKSISSFFAKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12060.t1 | Gene3D | G3DSA:2.20.25.530 | - | 17 | 83 | 4.3E-8 |
| 5 | g12060.t1 | Gene3D | G3DSA:1.10.20.120 | - | 84 | 217 | 4.6E-27 |
| 3 | g12060.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 259 | - |
| 4 | g12060.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 266 | - |
| 2 | g12060.t1 | PANTHER | PTHR13383 | RIBONUCLEASE H2 SUBUNIT B | 4 | 291 | 7.4E-35 |
| 1 | g12060.t1 | Pfam | PF17745 | Ydr279p protein triple barrel domain | 25 | 85 | 8.0E-7 |
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:0032299 | ribonuclease H2 complex | CC |
KEGG
Orthology
- This transcript has been annotated with K10744 (ribonuclease H2 subunit B)
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.
