General information for g3581.t4
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.t4 | TSS | g3581.t4 | 26533742 | 26533742 |
| chr_3 | g3581 | g3581.t4 | isoform | g3581.t4 | 26533814 | 26534728 |
| chr_3 | g3581 | g3581.t4 | exon | g3581.t4.exon1 | 26533814 | 26533911 |
| chr_3 | g3581 | g3581.t4 | cds | g3581.t4.CDS1 | 26533814 | 26533911 |
| chr_3 | g3581 | g3581.t4 | exon | g3581.t4.exon2 | 26533998 | 26534172 |
| chr_3 | g3581 | g3581.t4 | cds | g3581.t4.CDS2 | 26533998 | 26534172 |
| chr_3 | g3581 | g3581.t4 | exon | g3581.t4.exon3 | 26534230 | 26534449 |
| chr_3 | g3581 | g3581.t4 | cds | g3581.t4.CDS3 | 26534230 | 26534449 |
| chr_3 | g3581 | g3581.t4 | exon | g3581.t4.exon4 | 26534514 | 26534728 |
| chr_3 | g3581 | g3581.t4 | cds | g3581.t4.CDS4 | 26534514 | 26534728 |
| chr_3 | g3581 | g3581.t4 | TTS | g3581.t4 | 26534771 | 26534771 |
Sequences
>g3581.t4 Gene=g3581 Length=708
ATGGCACAAGAGTTATTGTCACTTCAAGGATTGCGTATTGACGGTCGCAGACAAAATGAA
TTAAGACAAATTCAATGTAGATTAGGAGTTTTAGAAAGATGTGATGGAAGTGCATATATG
CTTCATGGTAATACTAAAGTTATAGCATCAATATCAGGACCAAAACATCCAACAAAAAAT
AGTGCAAACAAAAATAGAGGAGGTGATGAATTTATATTTAATGTGCGTGTTAAATTTGCA
ACATTTTCCAAGAATGGAGAACGACAGAAGGTATCCGTCATTCTTGTGGAAAAATATGAG
AAATCACAGTTGGATCTTAACATAGAGATTCTTCAAACTGATGGAAGTGAAATATGCACA
GTAGTAAATGCTGCAACTCTTGCTCTCATAGATGCTGGAATTTGTATGAAAGAATATATT
TGTGCATGTACTGCATCTCTTACAAACGATGGAGTTGCGCTATTAGATGTTTCACATCTT
GAGGAAATATGTGGTGGACCAACATTAACAATCGCAGCGCTACCGAGAACAGGGGATCAT
GAACAAAGTGTGGCTTATGTGGAATTGTCTCAAAAATTCTACCTGAAAGATCTTAATAAA
ATTTTTGATTGCGCATTGATGGGCTGTGAAAAAATAAGAGGAATTCTAGACGAGGCAATT
CGATCTAACGCATTTGAGCTTGTAAATTCAGAATTGACAAACAATTGA
>g3581.t4 Gene=g3581 Length=235
MAQELLSLQGLRIDGRRQNELRQIQCRLGVLERCDGSAYMLHGNTKVIASISGPKHPTKN
SANKNRGGDEFIFNVRVKFATFSKNGERQKVSVILVEKYEKSQLDLNIEILQTDGSEICT
VVNAATLALIDAGICMKEYICACTASLTNDGVALLDVSHLEEICGGPTLTIAALPRTGDH
EQSVAYVELSQKFYLKDLNKIFDCALMGCEKIRGILDEAIRSNAFELVNSELTNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3581.t4 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 1 | 229 | 0e+00 |
| 3 | g3581.t4 | PANTHER | PTHR11953 | EXOSOME COMPLEX COMPONENT | 4 | 227 | 0e+00 |
| 4 | g3581.t4 | PANTHER | PTHR11953:SF0 | EXOSOME COMPLEX COMPONENT RRP41 | 4 | 227 | 0e+00 |
| 2 | g3581.t4 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 20 | 88 | 0e+00 |
| 1 | g3581.t4 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 92 | 134 | 3e-07 |
| 5 | g3581.t4 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 9 | 163 | 0e+00 |
| 6 | g3581.t4 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 136 | 227 | 0e+00 |
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 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.
