General information for g3581.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Exosome complex component RRP41.
Parent gene
- The parent gene g3581 is located on chr_3: 26533996..26534728 (+ 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_3 | g3581 | g3581.t1 | TSS | g3581.t1 | 26533742 | 26533742 |
| chr_3 | g3581 | g3581.t1 | isoform | g3581.t1 | 26533814 | 26534728 |
| chr_3 | g3581 | g3581.t1 | exon | g3581.t1.exon1 | 26533814 | 26533911 |
| chr_3 | g3581 | g3581.t1 | cds | g3581.t1.CDS1 | 26533814 | 26533911 |
| chr_3 | g3581 | g3581.t1 | exon | g3581.t1.exon2 | 26533998 | 26534449 |
| chr_3 | g3581 | g3581.t1 | cds | g3581.t1.CDS2 | 26533998 | 26534449 |
| chr_3 | g3581 | g3581.t1 | exon | g3581.t1.exon3 | 26534514 | 26534728 |
| chr_3 | g3581 | g3581.t1 | cds | g3581.t1.CDS3 | 26534514 | 26534728 |
| chr_3 | g3581 | g3581.t1 | TTS | g3581.t1 | 26534771 | 26534771 |
Sequences
>g3581.t1 Gene=g3581 Length=765
ATGGCACAAGAGTTATTGTCACTTCAAGGATTGCGTATTGACGGTCGCAGACAAAATGAA
TTAAGACAAATTCAATGTAGATTAGGAGTTTTAGAAAGATGTGATGGAAGTGCATATATG
CTTCATGGTAATACTAAAGTTATAGCATCAATATCAGGACCAAAACATCCAACAAAAAAT
AGTGCAAACAAAAATAGAGGAGGTGATGAATTTATATTTAATGTGCGTGTTAAATTTGCA
ACATTTTCCAAGAATGGAGAACGACAGAAGGTAGTAAAGAATAGCAAGAAACTTGGTGAG
ATTGAAATAAATTTAAAAAATATATTCAAATCCGTCATTCTTGTGGAAAAATATGAGAAA
TCACAGTTGGATCTTAACATAGAGATTCTTCAAACTGATGGAAGTGAAATATGCACAGTA
GTAAATGCTGCAACTCTTGCTCTCATAGATGCTGGAATTTGTATGAAAGAATATATTTGT
GCATGTACTGCATCTCTTACAAACGATGGAGTTGCGCTATTAGATGTTTCACATCTTGAG
GAAATATGTGGTGGACCAACATTAACAATCGCAGCGCTACCGAGAACAGGGGATCATGAA
CAAAGTGTGGCTTATGTGGAATTGTCTCAAAAATTCTACCTGAAAGATCTTAATAAAATT
TTTGATTGCGCATTGATGGGCTGTGAAAAAATAAGAGGAATTCTAGACGAGGCAATTCGA
TCTAACGCATTTGAGCTTGTAAATTCAGAATTGACAAACAATTGA
>g3581.t1 Gene=g3581 Length=254
MAQELLSLQGLRIDGRRQNELRQIQCRLGVLERCDGSAYMLHGNTKVIASISGPKHPTKN
SANKNRGGDEFIFNVRVKFATFSKNGERQKVVKNSKKLGEIEINLKNIFKSVILVEKYEK
SQLDLNIEILQTDGSEICTVVNAATLALIDAGICMKEYICACTASLTNDGVALLDVSHLE
EICGGPTLTIAALPRTGDHEQSVAYVELSQKFYLKDLNKIFDCALMGCEKIRGILDEAIR
SNAFELVNSELTNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3581.t1 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 1 | 248 | 0 |
| 2 | g3581.t1 | PANTHER | PTHR11953 | EXOSOME COMPLEX COMPONENT | 4 | 246 | 0 |
| 3 | g3581.t1 | PANTHER | PTHR11953:SF0 | EXOSOME COMPLEX COMPONENT RRP41 | 4 | 246 | 0 |
| 1 | g3581.t1 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 20 | 153 | 0 |
| 4 | g3581.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 9 | 182 | 0 |
| 5 | g3581.t1 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 155 | 246 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K11600 (exosome complex component RRP41)
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.
