General information for g6409.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Poly(A)-specific ribonuclease PARN.
Parent gene
- The parent gene g6409 is located on chr_2: 16881171..16882331 (- 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 | g6409 | g6409.t1 | isoform | g6409.t1 | 16880612 | 16882331 |
| chr_2 | g6409 | g6409.t1 | exon | g6409.t1.exon1 | 16880612 | 16882254 |
| chr_2 | g6409 | g6409.t1 | cds | g6409.t1.CDS1 | 16880612 | 16882254 |
| chr_2 | g6409 | g6409.t1 | exon | g6409.t1.exon2 | 16882313 | 16882331 |
| chr_2 | g6409 | g6409.t1 | cds | g6409.t1.CDS2 | 16882313 | 16882331 |
| chr_2 | g6409 | g6409.t1 | TSS | g6409.t1 | 16882430 | 16882430 |
| chr_2 | g6409 | g6409.t1 | TTS | g6409.t1 | NA | NA |
Sequences
>g6409.t1 Gene=g6409 Length=1662
ATGGAAGTTACAAAGCAAAATTTTAAAGATTGTCTCGTTGAAATTACAAAAGATATTGAA
GAAGCTCATTTTATTAGTATTGATACTGAATTTACCGGATTGACAAGCGAGCGAAATATT
TTGCCATTTGACACGAGTGAAGAATACTATGAAAAACTTTTCCGATCAACAAAAGGTTTT
ATTATAGTGCAATTAGGGATCTCATTATTTAAAAAAGATCCAGGTGGAGAAAAAGTGAAA
GTAAAATCTTACAATATTTACACTTACCCGCAATCGAGTCTTGCTACTTTTCTTTGTCAA
AGCCAATCATTTTCATTTTTAGCCGAAAATGGTTTTGATTTCAATAAATTGTTCTCTAGT
GGTGTCGGCGTTTGTAATGAAAAACAAGAAGAAAAGTTAAGACAAGAAGTTAAAGAACGT
CAAGAATTTAGACAAGAACAGATAAAAATACGTACAAGTGATGAACAAGTTGATACAAGT
AGCAGAAATTTTTTACCTGTACCTGAAAATGAAAAAGAGTTAATTGACAATGCAAAGGAG
AAGATTCAACAAGTGATTGATAATAAAATTCTTGAGGCAAAATTTGAGAAACTCAATGGT
TTCCAAAGGAAATTGATGTATGAACTAATTGAAAGAGATTTTAACAATAAAGTCTCTACA
TTGACTAAAAATGGAGATAATTATCAAAAAATGATGGTAGTTACTTCTAAAAGAACTCTT
GAAGATGAATTAAAATTGGAAAAGGACAAAATTCGGGACGATGAAAATTCTTTGATTGAA
AAAATTGGTATTCGTTTATTAATGAAAGAAATTTCTAAGTCAAAAAAGCCTATTGTGGCT
CATAACTGTTTATTAGACTTCTTCTACATCTTAACGCAATGTTTTGAAGATTTACCAGAA
AATTATAATGATTTCAAGAAACTTATTCATCGCATATTCCCAAACATTATTGATACAAAG
TTTATTGCACACTCTGACCACTTGAAAGAATTCTTCTCATCGACTGTATTAAATCAAGTT
CTTGAACGTCTACAGAAACCTCCATTCAAGGAAATTGAATTAGAATGGGAAAATCCTTAT
AATACATATAGTTTAAAATCACCGAAAGAGCATGAAGCTGGATATGATTCATTTTTGACT
GGATATTGCTTTTTAGCATTACTTGATCATCTCAATGTGCCTCTGGAATTAAACTTTGAG
AAATCTAAAGCATTAGCTCCATTTCTTAATCGTATTGCTCTTCAACGCATAGCTTTACCT
TACATTCACATTACAGGCGATGAGCCTAAATTAAATCGAACTCATGTATTTCATATTAAA
TTTCCACAAACATGGCAAGTTTCAGACATTCAAGATCATTTTAAAAATTATGGACCAATA
CAAATTTCATGGGTAGACAATACAACTGCATTTGTTGCACTTTATAATAAAGAAAACAGC
AGTTGTGTTTTAAAGACGATTGGAAAAGTTAATGGGTTTGAAATCAAGACATTTGCTGAT
TTTCAAGCGAATGAAAAAATCGTTTTATTAAAACAGAAGACTCTTAAACGAAAGAATGAA
GATTCAGAATCAGAAAGTACAAGTTCAAATACTACACCATCCAAACCTGAGGCGAAGCGC
AAGAAGAAGAAAGATACATTCAAGCAATGTAATAACTGGTAG
>g6409.t1 Gene=g6409 Length=553
MEVTKQNFKDCLVEITKDIEEAHFISIDTEFTGLTSERNILPFDTSEEYYEKLFRSTKGF
IIVQLGISLFKKDPGGEKVKVKSYNIYTYPQSSLATFLCQSQSFSFLAENGFDFNKLFSS
GVGVCNEKQEEKLRQEVKERQEFRQEQIKIRTSDEQVDTSSRNFLPVPENEKELIDNAKE
KIQQVIDNKILEAKFEKLNGFQRKLMYELIERDFNNKVSTLTKNGDNYQKMMVVTSKRTL
EDELKLEKDKIRDDENSLIEKIGIRLLMKEISKSKKPIVAHNCLLDFFYILTQCFEDLPE
NYNDFKKLIHRIFPNIIDTKFIAHSDHLKEFFSSTVLNQVLERLQKPPFKEIELEWENPY
NTYSLKSPKEHEAGYDSFLTGYCFLALLDHLNVPLELNFEKSKALAPFLNRIALQRIALP
YIHITGDEPKLNRTHVFHIKFPQTWQVSDIQDHFKNYGPIQISWVDNTTAFVALYNKENS
SCVLKTIGKVNGFEIKTFADFQANEKIVLLKQKTLKRKNEDSESESTSSNTTPSKPEAKR
KKKKDTFKQCNNW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6409.t1 | Coils | Coil | Coil | 126 | 146 | - |
| 13 | g6409.t1 | Coils | Coil | Coil | 237 | 257 | - |
| 10 | g6409.t1 | Gene3D | G3DSA:3.30.420.10 | - | 2 | 388 | 2.5E-103 |
| 12 | g6409.t1 | Gene3D | G3DSA:3.30.1370.50 | - | 155 | 239 | 2.5E-103 |
| 11 | g6409.t1 | Gene3D | G3DSA:3.30.70.330 | - | 422 | 513 | 3.9E-24 |
| 8 | g6409.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 515 | 553 | - |
| 9 | g6409.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 535 | 553 | - |
| 3 | g6409.t1 | PANTHER | PTHR15092 | POLY A -SPECIFIC RIBONUCLEASE/TARGET OF EGR1, MEMBER 1 | 1 | 540 | 3.1E-122 |
| 4 | g6409.t1 | PANTHER | PTHR15092:SF44 | POLY(A)-SPECIFIC RIBONUCLEASE PARN | 1 | 540 | 3.1E-122 |
| 2 | g6409.t1 | Pfam | PF04857 | CAF1 family ribonuclease | 3 | 384 | 4.6E-81 |
| 1 | g6409.t1 | Pfam | PF08675 | RNA binding domain | 426 | 503 | 3.5E-28 |
| 6 | g6409.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 1 | 391 | 4.55E-59 |
| 7 | g6409.t1 | SUPERFAMILY | SSF82708 | R3H domain | 164 | 247 | 8.24E-12 |
| 5 | g6409.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 420 | 489 | 3.46E-9 |
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 transcript has been annotated with K01148 (poly(A)-specific ribonuclease)
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.
