General information for g5786.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g5786 is located on chr_2: 11937230..11937661 (- 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 | g5786 | g5786.t1 | TTS | g5786.t1 | 11936936 | 11936936 |
| chr_2 | g5786 | g5786.t1 | isoform | g5786.t1 | 11937230 | 11937661 |
| chr_2 | g5786 | g5786.t1 | exon | g5786.t1.exon1 | 11937230 | 11937331 |
| chr_2 | g5786 | g5786.t1 | cds | g5786.t1.CDS1 | 11937230 | 11937331 |
| chr_2 | g5786 | g5786.t1 | exon | g5786.t1.exon2 | 11937399 | 11937518 |
| chr_2 | g5786 | g5786.t1 | cds | g5786.t1.CDS2 | 11937399 | 11937518 |
| chr_2 | g5786 | g5786.t1 | exon | g5786.t1.exon3 | 11937593 | 11937661 |
| chr_2 | g5786 | g5786.t1 | cds | g5786.t1.CDS3 | 11937593 | 11937661 |
| chr_2 | g5786 | g5786.t1 | TSS | g5786.t1 | 11937754 | 11937754 |
Sequences
>g5786.t1 Gene=g5786 Length=291
ATGAGATTCTGTGGTCCTAAATTATCGCTTTGCGGTCTGATCATCTCAGTATGGGGTATT
ATTCAATTGCTGCTTATGGGTGTCTTTTACTACATTCATAGTGTGGCGCTTATTGAAGAT
TTGCCAATTGAGGAGCATTATCACACTGCAGAAGAGTTTTATGCTGCTGCAGACCGAGCA
TATAGACAAAATGCACTCAACTGTTGGATTGCTGCTTTGATTTATGTCGTCACTTTAGCA
ATTTCTACTTGGCAATTCTATGCTAATCAACGTGCAAGCTCTGTAAATTAA
>g5786.t1 Gene=g5786 Length=96
MRFCGPKLSLCGLIISVWGIIQLLLMGVFYYIHSVALIEDLPIEEHYHTAEEFYAAADRA
YRQNALNCWIAALIYVVTLAISTWQFYANQRASSVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 1 | g5786.t1 | PANTHER | PTHR31733 | RIBONUCLEASE KAPPA | 2 | 94 | 2.4E-26 |
| 2 | g5786.t1 | PANTHER | PTHR31733:SF1 | RIBONUCLEASE KAPPA | 2 | 94 | 2.4E-26 |
| 5 | g5786.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 8 | g5786.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 32 | - |
| 7 | g5786.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 68 | - |
| 9 | g5786.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 87 | - |
| 6 | g5786.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 88 | 96 | - |
| 4 | g5786.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 10 | 32 | - |
| 3 | g5786.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5786/g5786.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5786.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004521 | endoribonuclease activity | MF |
| GO:0090305 | nucleic acid phosphodiester bond hydrolysis | BP |
KEGG
Orthology
- This transcript has been annotated with K19770 (ribonuclease kappa [EC:3.1.-.-])
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.
