General information for g4062.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Signal recognition particle 14 kDa protein.
Parent gene
- The parent gene g4062 is located on chr_3: 30317001..30318287 (+ 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 | g4062 | g4062.t1 | TSS | g4062.t1 | 30316494 | 30316494 |
| chr_3 | g4062 | g4062.t1 | isoform | g4062.t1 | 30316561 | 30317001 |
| chr_3 | g4062 | g4062.t1 | exon | g4062.t1.exon1 | 30316561 | 30316584 |
| chr_3 | g4062 | g4062.t1 | cds | g4062.t1.CDS1 | 30316561 | 30316584 |
| chr_3 | g4062 | g4062.t1 | exon | g4062.t1.exon2 | 30316640 | 30316712 |
| chr_3 | g4062 | g4062.t1 | cds | g4062.t1.CDS2 | 30316640 | 30316712 |
| chr_3 | g4062 | g4062.t1 | exon | g4062.t1.exon3 | 30316769 | 30317001 |
| chr_3 | g4062 | g4062.t1 | cds | g4062.t1.CDS3 | 30316769 | 30317001 |
| chr_3 | g4062 | g4062.t1 | TTS | g4062.t1 | 30317018 | 30317018 |
Sequences
>g4062.t1 Gene=g4062 Length=330
ATGGTTCTTTTGCAATATAATGAGTTTCTCACTCAAGTCACTATTTTAGCTCAAAAAGTT
CGAAATCAAAGTGCATTCACAATCACATTCAAACAATATGATGGAATAGATAAACCAACG
CCGAGAGAAGGCAAACCATCACATGCAGAACCTGCCGAAAATTATTGTCTAATTAGAATG
AAAGTAAAGAACAAGAAACTCTCAACTATTGTTAAGAAATCGGATATTACAAAAGTTATG
GAGTCTTATGGAAAAATAATGAAAGGTAATATGGATGGGTTAAAGAAAGTGAAGCGAGTC
AAAAATAAAACAAAAGCCAATCAAGGATGA
>g4062.t1 Gene=g4062 Length=109
MVLLQYNEFLTQVTILAQKVRNQSAFTITFKQYDGIDKPTPREGKPSHAEPAENYCLIRM
KVKNKKLSTIVKKSDITKVMESYGKIMKGNMDGLKKVKRVKNKTKANQG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4062.t1 | Gene3D | G3DSA:3.30.720.10 | Signal recognition particle alu RNA binding heterodimer | 1 | 109 | 0 |
| 2 | g4062.t1 | PANTHER | PTHR12013 | SIGNAL RECOGNITION PARTICLE 14 KD PROTEIN | 1 | 106 | 0 |
| 3 | g4062.t1 | PANTHER | PTHR12013:SF2 | SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN | 1 | 106 | 0 |
| 1 | g4062.t1 | Pfam | PF02290 | Signal recognition particle 14kD protein | 4 | 94 | 0 |
| 4 | g4062.t1 | SUPERFAMILY | SSF54762 | Signal recognition particle alu RNA binding heterodimer, SRP9/14 | 1 | 96 | 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:0006614 | SRP-dependent cotranslational protein targeting to membrane | BP |
| GO:0005786 | signal recognition particle, endoplasmic reticulum targeting | CC |
| GO:0030942 | endoplasmic reticulum signal peptide binding | MF |
| GO:0048500 | signal recognition particle | CC |
| GO:0008312 | 7S RNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03104 (signal recognition particle subunit SRP14)
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.
