General information for g6418.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Poly(A)-specific ribonuclease PARN.
Parent gene
- The parent gene g6418 is located on chr_2: 16897931..16898656 (- 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 | g6418 | g6418.t1 | TTS | g6418.t1 | 16897461 | 16897461 |
| chr_2 | g6418 | g6418.t1 | isoform | g6418.t1 | 16897931 | 16898656 |
| chr_2 | g6418 | g6418.t1 | exon | g6418.t1.exon1 | 16897931 | 16898656 |
| chr_2 | g6418 | g6418.t1 | cds | g6418.t1.CDS1 | 16897931 | 16898656 |
| chr_2 | g6418 | g6418.t1 | TSS | g6418.t1 | NA | NA |
Sequences
>g6418.t1 Gene=g6418 Length=726
ATGGAGATAATTATCAAAAAAATGATGGTAGTTACTTCTAAAAGAACTCTTGAAGATGAA
TTAAAATTGGAAAAGGACAAAATTCGGGACGATGAAAATTCTTTGATTGAAAAAATTGGT
ATTCGTTTATTAATGAAAGAAATTTCTAAGTCAAAAAAGCCTATTGTGGCTCATAACTGT
TTATTAGACTTCTTCTACATCTTAACGCAATGTTTTGAAGATTTACCAGAAAATTATAAT
GATTTCAAGAAACTTATTCATCGCATATTCCCAAACATTATTGATACAAAGTTTATTGCA
CACTCTGACCACTTGAAAGAATTCTTCTCATCGACTGTATTAAATCAAGTTCTTGAACGT
CTACAGAAACCTCCATTCAAGGAAATTGAATTAGAATGGGAAAATCCTTATAACACATAT
AGTTTAAAATCACCGAAAGAGCATGAAGCTGGATATGATTCATTTTTGACTGGATATTGC
TTTTTAGCATTACTTGATCATCTCAATGTGCCTCTGGAATTAAACTTTGAGAAATCTAAA
GCATTAGCTCCATTTCTTAATCGTATTGCTCTTCAACGCATAGCTTTACCTTACATTCAC
ATTACAGGCGATGAGCCTAAATTAAATCGAACTCATGTATTTCATATTAAATTTCCACAA
ACATGGCAAGTTTCAGACATTCAAGATCATTTTAAAATTATGGACCAATACAAATTTCAT
GGGTAG
>g6418.t1 Gene=g6418 Length=241
MEIIIKKMMVVTSKRTLEDELKLEKDKIRDDENSLIEKIGIRLLMKEISKSKKPIVAHNC
LLDFFYILTQCFEDLPENYNDFKKLIHRIFPNIIDTKFIAHSDHLKEFFSSTVLNQVLER
LQKPPFKEIELEWENPYNTYSLKSPKEHEAGYDSFLTGYCFLALLDHLNVPLELNFEKSK
ALAPFLNRIALQRIALPYIHITGDEPKLNRTHVFHIKFPQTWQVSDIQDHFKIMDQYKFH
G
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6418.t1 | Coils | Coil | Coil | 14 | 34 | - |
| 6 | g6418.t1 | Gene3D | G3DSA:3.30.420.10 | - | 4 | 202 | 1.2E-53 |
| 7 | g6418.t1 | Gene3D | G3DSA:3.30.70.330 | - | 203 | 240 | 2.8E-7 |
| 3 | g6418.t1 | PANTHER | PTHR15092 | POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1 | 6 | 235 | 5.9E-49 |
| 4 | g6418.t1 | PANTHER | PTHR15092:SF44 | POLY(A)-SPECIFIC RIBONUCLEASE PARN | 6 | 235 | 5.9E-49 |
| 2 | g6418.t1 | Pfam | PF04857 | CAF1 family ribonuclease | 17 | 161 | 3.4E-38 |
| 1 | g6418.t1 | Pfam | PF08675 | RNA binding domain | 203 | 233 | 6.4E-8 |
| 5 | g6418.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 37 | 168 | 1.52E-26 |
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:0004535 | poly(A)-specific ribonuclease activity | MF |
| GO:0046872 | metal ion binding | MF |
| GO:0005634 | nucleus | CC |
| GO:0003723 | RNA binding | MF |
| GO:0005737 | cytoplasm | CC |
| GO:0006402 | mRNA catabolic process | BP |
| GO:0003676 | nucleic acid binding | MF |
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.
