General information for g7941.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Exosome complex component RRP42.
Parent gene
- The parent gene g7941 is located on chr_2: 27138440..27139867 (+ 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 | g7941 | g7941.t1 | TSS | g7941.t1 | 27137432 | 27137432 |
| chr_2 | g7941 | g7941.t1 | isoform | g7941.t1 | 27137493 | 27138440 |
| chr_2 | g7941 | g7941.t1 | exon | g7941.t1.exon1 | 27137493 | 27137606 |
| chr_2 | g7941 | g7941.t1 | cds | g7941.t1.CDS1 | 27137493 | 27137606 |
| chr_2 | g7941 | g7941.t1 | exon | g7941.t1.exon2 | 27137676 | 27138440 |
| chr_2 | g7941 | g7941.t1 | cds | g7941.t1.CDS2 | 27137676 | 27138440 |
| chr_2 | g7941 | g7941.t1 | TTS | g7941.t1 | 27138552 | 27138552 |
Sequences
>g7941.t1 Gene=g7941 Length=879
ATGGCTTATAATGCCCTAAGCGAAGCAGAAAAGGTATTTATTCTTCATGGAATTCAAGAC
GACTTTAGAAATGATGGCAGATCGAGAAGAGATTTTCGTCCTATGGAATTACAGACTAAT
GTGATAGCAAGTGCTTGTGGCAGTGCAAGATTCTGTATAGCAAACTCAGATATTCTTGTA
GGAATAAAGCCAGAAATTGATGCTCCATTTCCTGATAAACCAGAGGAGGGAAAAATTGAA
TTTCATGTCGATTGTTCTGCAAATGCTTTGTTAGATTTTGAAGGTAGAGGAGGTGAGGAA
CTAGCATTAGAAATATCTAATTGCCTCCGAATTACCTACGCATCGCCCTTTGCATTTGAT
CTAAAATCCTTATGCATTTTACCAAAACATCAATGTTGGAAACTTTATGTTGATATTTTA
ATCCTTCAATGTGCCGGCAACCTATACGATGCAATTTCATTTGCTGTAAAAAGTGCATTT
TATAATCTTAGAATACCACGTGTGAATAGTGCTTTATTAGACGGAGGAAATGTAGATCTT
GTTCTTTCTGATGATCCATCAGACTGTGACCGGTTAGATGTTCAATCGATCCCAATTCTG
CTTACAATTTGCAAAATTGGTGAACATTGTGTCATTGATCCGTCTATTGATGAAGAAATC
TGCAGTTCATCAAACATTGTTGTGGGGGTCAGTAGGAACAAAATCGTTTCTTTGAAAACG
ATAAGTGGAGGGTCATTTCACCCTGACACAATCGAAAACTGTATTGATCTAGCTATTTCG
ACTGCAAAAACTTTAGATAATACACTGATGAATATTCTGAAACACGAAGAGAGTTTAACA
AAGTCAAAGAAAAATATAAAATGTTCTTTTCTTAATTAA
>g7941.t1 Gene=g7941 Length=292
MAYNALSEAEKVFILHGIQDDFRNDGRSRRDFRPMELQTNVIASACGSARFCIANSDILV
GIKPEIDAPFPDKPEEGKIEFHVDCSANALLDFEGRGGEELALEISNCLRITYASPFAFD
LKSLCILPKHQCWKLYVDILILQCAGNLYDAISFAVKSAFYNLRIPRVNSALLDGGNVDL
VLSDDPSDCDRLDVQSIPILLTICKIGEHCVIDPSIDEEICSSSNIVVGVSRNKIVSLKT
ISGGSFHPDTIENCIDLAISTAKTLDNTLMNILKHEESLTKSKKNIKCSFLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7941.t1 | CDD | cd11367 | RNase_PH_RRP42 | 5 | 274 | 0 |
| 7 | g7941.t1 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 5 | 291 | 0 |
| 3 | g7941.t1 | PANTHER | PTHR11097:SF8 | EXOSOME COMPLEX COMPONENT RRP42 | 5 | 277 | 0 |
| 4 | g7941.t1 | PANTHER | PTHR11097 | EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN | 5 | 277 | 0 |
| 2 | g7941.t1 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 31 | 166 | 0 |
| 1 | g7941.t1 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 197 | 259 | 0 |
| 5 | g7941.t1 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 4 | 220 | 0 |
| 6 | g7941.t1 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 192 | 281 | 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 K12589 (exosome complex component RRP42)
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.
