General information for g6419.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 g6419 is located on chr_2: 16898711..16899383 (- 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 | g6419 | g6419.t1 | isoform | g6419.t1 | 16898711 | 16899383 |
| chr_2 | g6419 | g6419.t1 | exon | g6419.t1.exon1 | 16898711 | 16899003 |
| chr_2 | g6419 | g6419.t1 | cds | g6419.t1.CDS1 | 16898711 | 16899003 |
| chr_2 | g6419 | g6419.t1 | exon | g6419.t1.exon2 | 16899104 | 16899307 |
| chr_2 | g6419 | g6419.t1 | cds | g6419.t1.CDS2 | 16899104 | 16899307 |
| chr_2 | g6419 | g6419.t1 | exon | g6419.t1.exon3 | 16899365 | 16899383 |
| chr_2 | g6419 | g6419.t1 | cds | g6419.t1.CDS3 | 16899365 | 16899383 |
| chr_2 | g6419 | g6419.t1 | TSS | g6419.t1 | NA | NA |
| chr_2 | g6419 | g6419.t1 | TTS | g6419.t1 | NA | NA |
Sequences
>g6419.t1 Gene=g6419 Length=516
ATGGAAGTTACAAAGCAAAATTTTAAAGATTGTCTCGTTGAAATTACAAAAGATATTGAA
GAAGCTCATTTTATTAGTATTGATACTGAATTTACCGGATTGACAAGCGAGCGAAATATT
TTGCCATTTGACACGAGTGAAGAATACTATGAAAAACTTTTCCGATCAACAAAAGGTTTT
ATTATAGTGCAATTAGGGATCTCATTATTTAAAAAAGATCCAGCCGAAAATGTTTTTGAT
TTCAATAAATTGTTCTCTAGTGGTGTCGGCGTTTGTAATGAAAAACAAGAAGAAAAGTTA
AGACAAGAAGTTAAAGAACGTCAAGAATTTAGACAAGAACAGATAAAAATACGTACAAGT
GATGAACAAGTTGATACAAGTAGCAGAAATTTTTTACCTGTACCTGAAAATGAAAAAGAG
TTAATTGACAATGCAAAGGAGAAGATTCAACAAGTGATTGATATAAAATTCTTGAGGCAA
AATTTGAGAAACTCAATGGTTTCCAAAGGAAATTGA
>g6419.t1 Gene=g6419 Length=171
MEVTKQNFKDCLVEITKDIEEAHFISIDTEFTGLTSERNILPFDTSEEYYEKLFRSTKGF
IIVQLGISLFKKDPAENVFDFNKLFSSGVGVCNEKQEEKLRQEVKERQEFRQEQIKIRTS
DEQVDTSSRNFLPVPENEKELIDNAKEKIQQVIDIKFLRQNLRNSMVSKGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6419.t1 | Coils | Coil | Coil | 93 | 113 | - |
| 7 | g6419.t1 | Gene3D | G3DSA:3.30.420.10 | - | 1 | 128 | 2.3E-26 |
| 2 | g6419.t1 | PANTHER | PTHR15092 | POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1 | 1 | 77 | 8.9E-31 |
| 4 | g6419.t1 | PANTHER | PTHR15092:SF44 | POLY(A)-SPECIFIC RIBONUCLEASE PARN | 1 | 77 | 8.9E-31 |
| 3 | g6419.t1 | PANTHER | PTHR15092 | POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1 | 76 | 154 | 8.9E-31 |
| 5 | g6419.t1 | PANTHER | PTHR15092:SF44 | POLY(A)-SPECIFIC RIBONUCLEASE PARN | 76 | 154 | 8.9E-31 |
| 1 | g6419.t1 | Pfam | PF04857 | CAF1 family ribonuclease | 3 | 76 | 1.3E-19 |
| 6 | g6419.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 1 | 162 | 3.3E-19 |
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: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. There were no conditions that were differentially expressed