General information for g2470.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Signal recognition particle receptor subunit beta.
Parent gene
- The parent gene g2470 is located on chr_3: 18122965..18123802 (- 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 | g2470 | g2470.t2 | TTS | g2470.t2 | 18122923 | 18122923 |
| chr_3 | g2470 | g2470.t2 | isoform | g2470.t2 | 18122965 | 18123802 |
| chr_3 | g2470 | g2470.t2 | exon | g2470.t2.exon1 | 18122965 | 18123154 |
| chr_3 | g2470 | g2470.t2 | cds | g2470.t2.CDS1 | 18122965 | 18123154 |
| chr_3 | g2470 | g2470.t2 | exon | g2470.t2.exon2 | 18123216 | 18123802 |
| chr_3 | g2470 | g2470.t2 | cds | g2470.t2.CDS2 | 18123216 | 18123670 |
| chr_3 | g2470 | g2470.t2 | TSS | g2470.t2 | 18123878 | 18123878 |
Sequences
>g2470.t2 Gene=g2470 Length=777
ATGGATAAAGAGACAAGAAAAGAGCCAATTAGGCTCAGTGAAATCAATTTTACTCCCATT
CTCATTGCATTTGCTGTAGTTTTCTTAACATTAGGTAAAATCATAGTTTATTTTTGCAGA
AAATAAAAATTTATGCATGTTTTTCTTCCAGTTATCATCTATTTAATCAAAAAACGTAGT
CCAAGAAGAACAGACATTTTACTAGCTGGCTTATGTGATTCAGGAAAGACTCTTTTGTAT
TCATTGCTACTCAATGGAAATGAAGTCGAGACATTTACTTCATTAAAAGAAAATTGTGGA
ATTTTTCAAATTGAAGATAGCAAATCACTTCGTATTGTTGATCTTCCAGGCCATGAAAGA
CTTCGTTTGAGATTACTGGAAAATTATAAAAATTCAACAAAAGCCATCATCTACGTCGTT
GATTCAACTACTGTTCAAAAAGAGATTCGTGATGTTGCAGATTTCTTATACACATTACTC
GCTGATAAAGCACTTTCATCATTGAACGTTTTAATTTTGTGTAACAAGCAAGATGAGACC
ATGGCTAAAGGAAAACAAGTGGTTGAACAATTACTTGAAAAAGAAATTAATGTAATTCGA
AAGACAAGAACAAGCCAATTGCAGTCAGTTGATAATTCATCAGATAAAACAATGTACCTA
GGAAAAAGCGACAAAGACTTTGATTTTTCACAAATCTCACAGAAAATTTCATTTGCCGAA
TCATCAGCAAAGAATAAAGATATTGAACAAATAATTAGCTTCATAAAGGCTCTGTAA
>g2470.t2 Gene=g2470 Length=214
MHVFLPVIIYLIKKRSPRRTDILLAGLCDSGKTLLYSLLLNGNEVETFTSLKENCGIFQI
EDSKSLRIVDLPGHERLRLRLLENYKNSTKAIIYVVDSTTVQKEIRDVADFLYTLLADKA
LSSLNVLILCNKQDETMAKGKQVVEQLLEKEINVIRKTRTSQLQSVDNSSDKTMYLGKSD
KDFDFSQISQKISFAESSAKNKDIEQIISFIKAL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2470.t2 | CDD | cd04105 | SR_beta | 22 | 211 | 0.0000 |
| 6 | g2470.t2 | Gene3D | G3DSA:3.40.50.300 | - | 13 | 214 | 0.0000 |
| 2 | g2470.t2 | PANTHER | PTHR11485:SF34 | SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT BETA | 6 | 212 | 0.0000 |
| 3 | g2470.t2 | PANTHER | PTHR11485 | TRANSFERRIN | 6 | 212 | 0.0000 |
| 1 | g2470.t2 | Pfam | PF09439 | Signal recognition particle receptor beta subunit | 19 | 191 | 0.0000 |
| 7 | g2470.t2 | ProSiteProfiles | PS51417 | small GTPase Arf family profile. | 13 | 192 | 8.5650 |
| 5 | g2470.t2 | SMART | SM00177 | arf_sub_2 | 1 | 189 | 0.0092 |
| 4 | g2470.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 22 | 208 | 0.0000 |
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 K12272 (signal recognition particle receptor subunit beta)
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.
