General information for g7941.t3
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.t3 | TSS | g7941.t3 | 27137432 | 27137432 |
| chr_2 | g7941 | g7941.t3 | isoform | g7941.t3 | 27137493 | 27138440 |
| chr_2 | g7941 | g7941.t3 | exon | g7941.t3.exon1 | 27137493 | 27137607 |
| chr_2 | g7941 | g7941.t3 | cds | g7941.t3.CDS1 | 27137539 | 27137607 |
| chr_2 | g7941 | g7941.t3 | exon | g7941.t3.exon2 | 27137676 | 27138440 |
| chr_2 | g7941 | g7941.t3 | cds | g7941.t3.CDS2 | 27137676 | 27138440 |
| chr_2 | g7941 | g7941.t3 | TTS | g7941.t3 | 27138552 | 27138552 |
Sequences
>g7941.t3 Gene=g7941 Length=880
ATGGCTTATAATGCCCTAAGCGAAGCAGAAAAGGTATTTATTCTTCATGGAATTCAAGAC
GACTTTAGAAATGATGGCAGATCGAGAAGAGATTTTCGTCCTATGGAATTACAGGACTAA
TGTGATAGCAAGTGCTTGTGGCAGTGCAAGATTCTGTATAGCAAACTCAGATATTCTTGT
AGGAATAAAGCCAGAAATTGATGCTCCATTTCCTGATAAACCAGAGGAGGGAAAAATTGA
ATTTCATGTCGATTGTTCTGCAAATGCTTTGTTAGATTTTGAAGGTAGAGGAGGTGAGGA
ACTAGCATTAGAAATATCTAATTGCCTCCGAATTACCTACGCATCGCCCTTTGCATTTGA
TCTAAAATCCTTATGCATTTTACCAAAACATCAATGTTGGAAACTTTATGTTGATATTTT
AATCCTTCAATGTGCCGGCAACCTATACGATGCAATTTCATTTGCTGTAAAAAGTGCATT
TTATAATCTTAGAATACCACGTGTGAATAGTGCTTTATTAGACGGAGGAAATGTAGATCT
TGTTCTTTCTGATGATCCATCAGACTGTGACCGGTTAGATGTTCAATCGATCCCAATTCT
GCTTACAATTTGCAAAATTGGTGAACATTGTGTCATTGATCCGTCTATTGATGAAGAAAT
CTGCAGTTCATCAAACATTGTTGTGGGGGTCAGTAGGAACAAAATCGTTTCTTTGAAAAC
GATAAGTGGAGGGTCATTTCACCCTGACACAATCGAAAACTGTATTGATCTAGCTATTTC
GACTGCAAAAACTTTAGATAATACACTGATGAATATTCTGAAACACGAAGAGAGTTTAAC
AAAGTCAAAGAAAAATATAAAATGTTCTTTTCTTAATTAA
>g7941.t3 Gene=g7941 Length=277
MEFKTTLEMMADREEIFVLWNYRTNVIASACGSARFCIANSDILVGIKPEIDAPFPDKPE
EGKIEFHVDCSANALLDFEGRGGEELALEISNCLRITYASPFAFDLKSLCILPKHQCWKL
YVDILILQCAGNLYDAISFAVKSAFYNLRIPRVNSALLDGGNVDLVLSDDPSDCDRLDVQ
SIPILLTICKIGEHCVIDPSIDEEICSSSNIVVGVSRNKIVSLKTISGGSFHPDTIENCI
DLAISTAKTLDNTLMNILKHEESLTKSKKNIKCSFLN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g7941.t3 | CDD | cd11367 | RNase_PH_RRP42 | 23 | 259 | 0 |
| 7 | g7941.t3 | Gene3D | G3DSA:3.30.230.70 | GHMP Kinase | 20 | 276 | 0 |
| 3 | g7941.t3 | PANTHER | PTHR11097:SF8 | EXOSOME COMPLEX COMPONENT RRP42 | 23 | 262 | 0 |
| 4 | g7941.t3 | PANTHER | PTHR11097 | EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN | 23 | 262 | 0 |
| 2 | g7941.t3 | Pfam | PF01138 | 3’ exoribonuclease family, domain 1 | 23 | 151 | 0 |
| 1 | g7941.t3 | Pfam | PF03725 | 3’ exoribonuclease family, domain 2 | 182 | 244 | 0 |
| 5 | g7941.t3 | SUPERFAMILY | SSF54211 | Ribosomal protein S5 domain 2-like | 24 | 205 | 0 |
| 6 | g7941.t3 | SUPERFAMILY | SSF55666 | Ribonuclease PH domain 2-like | 177 | 266 | 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 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. There were no conditions that were differentially expressed