General information for g2470.t4
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.t4 | TTS | g2470.t4 | 18122923 | 18122923 |
| chr_3 | g2470 | g2470.t4 | isoform | g2470.t4 | 18122965 | 18123802 |
| chr_3 | g2470 | g2470.t4 | exon | g2470.t4.exon1 | 18122965 | 18123145 |
| chr_3 | g2470 | g2470.t4 | exon | g2470.t4.exon2 | 18123211 | 18123651 |
| chr_3 | g2470 | g2470.t4 | cds | g2470.t4.CDS1 | 18123212 | 18123651 |
| chr_3 | g2470 | g2470.t4 | exon | g2470.t4.exon3 | 18123709 | 18123802 |
| chr_3 | g2470 | g2470.t4 | cds | g2470.t4.CDS2 | 18123709 | 18123802 |
| chr_3 | g2470 | g2470.t4 | TSS | g2470.t4 | 18123878 | 18123878 |
Sequences
>g2470.t4 Gene=g2470 Length=716
ATGGATAAAGAGACAAGAAAAGAGCCAATTAGGCTCAGTGAAATCAATTTTACTCCCATT
CTCATTGCATTTGCTGTAGTTTTCTTAACATTAGTTATCATCTATTTAATCAAAAAACGT
AGTCCAAGAAGAACAGACATTTTACTAGCTGGCTTATGTGATTCAGGAAAGACTCTTTTG
TATTCATTGCTACTCAATGGAAATGAAGTCGAGACATTTACTTCATTAAAAGAAAATTGT
GGAATTTTTCAAATTGAAGATAGCAAATCACTTCGTATTGTTGATCTTCCAGGCCATGAA
AGACTTCGTTTGAGATTACTGGAAAATTATAAAAATTCAACAAAAGCCATCATCTACGTC
GTTGATTCAACTACTGTTCAAAAAGAGATTCGTGATGTTGCAGATTTCTTATACACATTA
CTCGCTGATAAAGCACTTTCATCATTGAACGTTTTAATTTTGTGTAACAAGCAAGATGAG
ACCATGGCTAAAGGAAAACAAGTGGTTGAACAATTACTTGAAAAAGAAATGTAAGTCGAA
AGACAAGAACAAGCCAATTGCAGTCAGTTGATAATTCATCAGATAAAACAATGTACCTAG
GAAAAAGCGACAAAGACTTTGATTTTTCACAAATCTCACAGAAAATTTCATTTGCCGAAT
CATCAGCAAAGAATAAAGATATTGAACAAATAATTAGCTTCATAAAGGCTCTGTAA
>g2470.t4 Gene=g2470 Length=177
MDKETRKEPIRLSEINFTPILIAFAVVFLTLVIIYLIKKRSPRRTDILLAGLCDSGKTLL
YSLLLNGNEVETFTSLKENCGIFQIEDSKSLRIVDLPGHERLRLRLLENYKNSTKAIIYV
VDSTTVQKEIRDVADFLYTLLADKALSSLNVLILCNKQDETMAKGKQVVEQLLEKEM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2470.t4 | CDD | cd04105 | SR_beta | 47 | 177 | 2.51322E-52 |
| 6 | g2470.t4 | Gene3D | G3DSA:3.40.50.300 | - | 38 | 177 | 7.0E-48 |
| 2 | g2470.t4 | PANTHER | PTHR11485:SF34 | SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT BETA | 10 | 177 | 4.6E-46 |
| 3 | g2470.t4 | PANTHER | PTHR11485 | TRANSFERRIN | 10 | 177 | 4.6E-46 |
| 1 | g2470.t4 | Pfam | PF09439 | Signal recognition particle receptor beta subunit | 44 | 177 | 2.2E-40 |
| 8 | g2470.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 19 | - |
| 9 | g2470.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 37 | - |
| 7 | g2470.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 38 | 177 | - |
| 5 | g2470.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 42 | 171 | 3.07E-22 |
| 4 | g2470.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
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.
