General information for g9634.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Exosome complex component RRP4.
Parent gene
- The parent gene g9634 is located on chr_1: 4375736..4376666 (- 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_1 | g9634 | g9634.t1 | TTS | g9634.t1 | 4375720 | 4375720 |
| chr_1 | g9634 | g9634.t1 | isoform | g9634.t1 | 4375736 | 4376666 |
| chr_1 | g9634 | g9634.t1 | exon | g9634.t1.exon1 | 4375736 | 4376492 |
| chr_1 | g9634 | g9634.t1 | cds | g9634.t1.CDS1 | 4375736 | 4376492 |
| chr_1 | g9634 | g9634.t1 | exon | g9634.t1.exon2 | 4376545 | 4376666 |
| chr_1 | g9634 | g9634.t1 | cds | g9634.t1.CDS2 | 4376545 | 4376666 |
| chr_1 | g9634 | g9634.t1 | TSS | g9634.t1 | 4376746 | 4376746 |
Sequences
>g9634.t1 Gene=g9634 Length=879
ATGGCTAACATTAAAATTAATTTGCTTATGAACAAAGCAAAATACACATCAGATCTTGGT
GAAAATAATTGCAGAATTTATACAACTGGAGAAGTTATAACAGAACAAAAAGATTTCATG
CGCGGACATGGAACATACGTTGAAGATGGTCTTATAAAATCATCGGTAGTTGGAGTTGTA
AGACAAATTAATAAGCTCATTTCTGTTGTTCCTTTAAAAAGTAAATATGTAGGAGAAATA
GGAGATGTTGTTATTGGTCGAGTTACTGAAATTCAAAAGAAACGATGGAAAATTGACACA
AACTCACGATTAGATTCTGTTTTATTAATATCTTCAATTAACTTACCTGGCGGTGAATTA
CGACGAAGAAATGCAGAAGATGAACAATCAATGAGAAAATTGCTACAAGAAGAAGATCTT
CTCTCTGCCGAAGTTCAGAATGTATATGTTGATGGAAGTTTATCACTGCATACGAGAAGT
TTAAAATATGGAAAATTATCACAAGGTATACTCATTTCAGTCTCACCATCACTCATTAAA
AGAAGAAAGAATCATTTTCATAATCTTCCATGTGGAGTATCAGTCATTATTGGAAATAAT
GGATACATTTGGATCAGTCCTATTGTTAATGTAGAAATTGAAGGTCAAGGTGGATTTGCA
CAAAGTTTAGATGCAATTTCAAAATCAGATCGTGAAGCAATTGTAAGAATTAAAAATTGT
GTGCAAGCTTTAGCATCATGCTATGTAATGATTTATGACACGAGCATTACATTCGCATAT
GAAGAATCTTTGAAATATGAAGCAAAAGAACTACTTAATCATGATACTATGTATGAAATT
GGTTTTAATACAAAATTAAAATTAATGCAACAAGAATAA
>g9634.t1 Gene=g9634 Length=292
MANIKINLLMNKAKYTSDLGENNCRIYTTGEVITEQKDFMRGHGTYVEDGLIKSSVVGVV
RQINKLISVVPLKSKYVGEIGDVVIGRVTEIQKKRWKIDTNSRLDSVLLISSINLPGGEL
RRRNAEDEQSMRKLLQEEDLLSAEVQNVYVDGSLSLHTRSLKYGKLSQGILISVSPSLIK
RRKNHFHNLPCGVSVIIGNNGYIWISPIVNVEIEGQGGFAQSLDAISKSDREAIVRIKNC
VQALASCYVMIYDTSITFAYEESLKYEAKELLNHDTMYEIGFNTKLKLMQQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g9634.t1 | CDD | cd05789 | S1_Rrp4 | 75 | 166 | 0 |
| 8 | g9634.t1 | Gene3D | G3DSA:2.40.50.100 | - | 25 | 76 | 0 |
| 9 | g9634.t1 | Gene3D | G3DSA:2.40.50.140 | - | 77 | 167 | 0 |
| 3 | g9634.t1 | PANTHER | PTHR21321:SF4 | EXOSOME COMPLEX COMPONENT RRP4 | 23 | 276 | 0 |
| 4 | g9634.t1 | PANTHER | PTHR21321 | PNAS-3 RELATED | 23 | 276 | 0 |
| 1 | g9634.t1 | Pfam | PF14382 | Exosome complex exonuclease RRP4 N-terminal region | 26 | 61 | 0 |
| 2 | g9634.t1 | Pfam | PF15985 | KH domain | 169 | 206 | 0 |
| 6 | g9634.t1 | SUPERFAMILY | SSF110324 | Ribosomal L27 protein-like | 25 | 74 | 0 |
| 7 | g9634.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 74 | 166 | 0 |
| 5 | g9634.t1 | SUPERFAMILY | SSF54791 | Eukaryotic type KH-domain (KH-domain type I) | 168 | 285 | 0 |
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:0003723 | RNA binding | MF |
| GO:0000178 | exosome (RNase complex) | CC |
KEGG
Orthology
- This transcript has been annotated with K03679 (exosome complex component RRP4)
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.
