General information for g2837.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Signal recognition particle receptor subunit alpha-like protein.
Parent gene
- The parent gene g2837 is located on chr_3: 20506376..20507239 (+ 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 | g2837 | g2837.t1 | TSS | g2837.t1 | 20504191 | 20504191 |
| chr_3 | g2837 | g2837.t1 | isoform | g2837.t1 | 20504264 | 20506376 |
| chr_3 | g2837 | g2837.t1 | exon | g2837.t1.exon1 | 20504264 | 20504380 |
| chr_3 | g2837 | g2837.t1 | cds | g2837.t1.CDS1 | 20504264 | 20504380 |
| chr_3 | g2837 | g2837.t1 | exon | g2837.t1.exon2 | 20504482 | 20505606 |
| chr_3 | g2837 | g2837.t1 | cds | g2837.t1.CDS2 | 20504482 | 20505606 |
| chr_3 | g2837 | g2837.t1 | exon | g2837.t1.exon3 | 20505673 | 20506191 |
| chr_3 | g2837 | g2837.t1 | cds | g2837.t1.CDS3 | 20505673 | 20506191 |
| chr_3 | g2837 | g2837.t1 | exon | g2837.t1.exon4 | 20506251 | 20506376 |
| chr_3 | g2837 | g2837.t1 | cds | g2837.t1.CDS4 | 20506251 | 20506376 |
| chr_3 | g2837 | g2837.t1 | TTS | g2837.t1 | 20506475 | 20506475 |
Sequences
>g2837.t1 Gene=g2837 Length=1887
ATGCTCGATTTGTTTACGATTTTCACTAAAGGAGGCATAGTTCTCTGGTGTTTCCGAAAT
ATAAATGAGCCTTTTGCACCATCAATCAATGCCTTGATCAAAAATATATTGATGCAGGAG
CGTGGAGGAAGCAACTCTTATGAGCACAACAACTTGACTCTTCAATATAAGCTCGATAAT
GAGTTTGAGTTGATATTCGTTGTTGCCTTTCAGAAGATTTTGCAACTCGCTTACATTGAC
AAGTTTCTATCAGACATTCATTTAGAATTTCGCGATAAATATAAGAATGAATTGACATCA
CAGGGTAGAGAATTTTACAACTTTAATTTGAGCGATGAATTCAAGAGAATATTAAAAGAA
GCAGAGGCATGGGGTCAAGTGCAAAAAAGCATTCCTCGTACCATGAGAACCTTCGATGAA
TCACACAAGTCAAAAAAGACTGTTGATTCTATGATTGTTCGAAAAAGTGGTGACGATAAG
TCCAATGTAAATACTAATAAAAAATCTGTCAAAATTGTTGAAACTGAAAAAGTCAATGCC
AAGAATGATGATTATGATGATATAAATGGAAATGCGGACAATGAGATTGCCTTGGCACGC
AAAAAACTTGCAGATAAGTTTACTAAAAAAAGTCCAGCTGATAAGAAGAAATCACCAAAA
TCATCATCATCATCTGAGAAGAAAAAGAAGACAGATCGTGTTTGGGAATTGAATGGAAAT
TCAAAAGATGCAATAACACTCGATCGTTCAAAAGATCGACCTGAAGATATAAAAAGTGAC
TTTACACATTTGGATAAAATGGTTGGTCAATCAATTGGTAATATAAAAGACATTGAAATA
GAGGAAGAATCATCTGAAGAAGAAGATTCAGATGAATATGAAGAAAAAGAAACAAAGTCA
CAAGCTAAGAAAGCATCACGTAGTGGAGGCATGTTGTCAATGTTTAAAGGACTTGTTGGA
TCAAAATCAATTACAATTGAAGATATGCAACCAGCTCTTGATAAATTGAGAGATCATTTG
ATTGCAAAAAATGTTGCTACTGATATATCGCAAAAATTGTGTGCTTCTGTTGCTGCAAAA
TTGGAGGGAAAAGTTTTGGGTACATTTGATACAATTGCAGCAACTGTTAAAACTACTTTG
AATGATTCTTTGGTTCAAATTCTTTCACCAAAACGACGTATTGACATTCTTCGTGATTGC
TTAGAGGCAAAAAGAAATAATAGGCCATATGTTATGACATTCTGTGGTGTCAATGGTGTA
GGCAAATCAACAAATTTGGCAAAAATCTGTTTCTGGTTGATTGAGAATAACTTCAATGTA
TTGATTGCAGCTTGTGACACTTTTCGTGCGGGTGCTGTTGAACAGTTGCGCACACATACT
CGTCATTTGAATGCACTTCATCCAAAAGAAAAGCATGGAGGTCGTGAGATGGTTGAGTTA
TATGAAAAAGGATATGGCAAAGATGCAGCAGGAATAGCAATGGAAGCGATTCGTTATGCT
AAAGAAGCAGGAATTGATGTTGTTCTTGTTGATACTGCTGGTCGAATGCAAGACAATGAA
CCTTTGATGCGCGCACTTGCTAAACTGATCAAAATTAATGAGCCTGATTTGGTATTATTC
GTTGGTGAGGCTCTTGTTGGAAATGAAGCTGTCGATCAATTGGTGAAATTTAATCAAGCT
CTTGCTGATCATTCTTCAATGGAAAATCCTCATGTTATTGATGGAATCGTTTTAACTAAA
TTTGACACTATTGATGATAAGGTTGGTGCCGCAATTTCAATGACATACATCACAGGTCAA
CCAATTGTTTTCGTTGGTACTGGTCAAACGTATACCGATTTAAAGGCTTTAAATGCACGT
GCCGTTGTTCATGCACTCATGAAATAA
>g2837.t1 Gene=g2837 Length=628
MLDLFTIFTKGGIVLWCFRNINEPFAPSINALIKNILMQERGGSNSYEHNNLTLQYKLDN
EFELIFVVAFQKILQLAYIDKFLSDIHLEFRDKYKNELTSQGREFYNFNLSDEFKRILKE
AEAWGQVQKSIPRTMRTFDESHKSKKTVDSMIVRKSGDDKSNVNTNKKSVKIVETEKVNA
KNDDYDDINGNADNEIALARKKLADKFTKKSPADKKKSPKSSSSSEKKKKTDRVWELNGN
SKDAITLDRSKDRPEDIKSDFTHLDKMVGQSIGNIKDIEIEEESSEEEDSDEYEEKETKS
QAKKASRSGGMLSMFKGLVGSKSITIEDMQPALDKLRDHLIAKNVATDISQKLCASVAAK
LEGKVLGTFDTIAATVKTTLNDSLVQILSPKRRIDILRDCLEAKRNNRPYVMTFCGVNGV
GKSTNLAKICFWLIENNFNVLIAACDTFRAGAVEQLRTHTRHLNALHPKEKHGGREMVEL
YEKGYGKDAAGIAMEAIRYAKEAGIDVVLVDTAGRMQDNEPLMRALAKLIKINEPDLVLF
VGEALVGNEAVDQLVKFNQALADHSSMENPHVIDGIVLTKFDTIDDKVGAAISMTYITGQ
PIVFVGTGQTYTDLKALNARAVVHALMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g2837.t1 | CDD | cd14826 | SR_alpha_SRX | 3 | 120 | 2.59166E-47 |
| 12 | g2837.t1 | CDD | cd17876 | SRalpha_C | 410 | 626 | 3.5614E-146 |
| 10 | g2837.t1 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 126 | 3.3E-44 |
| 11 | g2837.t1 | Gene3D | G3DSA:1.20.120.140 | - | 278 | 390 | 5.3E-23 |
| 9 | g2837.t1 | Gene3D | G3DSA:3.40.50.300 | - | 393 | 628 | 1.7E-93 |
| 18 | g2837.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 207 | 237 | - |
| 20 | g2837.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 272 | 307 | - |
| 19 | g2837.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 280 | 294 | - |
| 4 | g2837.t1 | PANTHER | PTHR43134:SF1 | SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA | 1 | 628 | 2.6E-234 |
| 5 | g2837.t1 | PANTHER | PTHR43134 | SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA | 1 | 628 | 2.6E-234 |
| 1 | g2837.t1 | Pfam | PF04086 | Signal recognition particle, alpha subunit, N-terminal | 29 | 282 | 3.4E-51 |
| 2 | g2837.t1 | Pfam | PF02881 | SRP54-type protein, helical bundle domain | 309 | 380 | 7.8E-9 |
| 3 | g2837.t1 | Pfam | PF00448 | SRP54-type protein, GTPase domain | 410 | 627 | 4.5E-48 |
| 14 | g2837.t1 | ProSitePatterns | PS00300 | SRP54-type proteins GTP-binding domain signature. | 601 | 614 | - |
| 15 | g2837.t1 | SMART | SM00963 | SRP54_N_2 | 314 | 388 | 3.8E-6 |
| 16 | g2837.t1 | SMART | SM00382 | AAA_5 | 408 | 561 | 9.0E-8 |
| 17 | g2837.t1 | SMART | SM00962 | SRP54_3 | 409 | 628 | 1.2E-83 |
| 7 | g2837.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 124 | 2.04E-39 |
| 6 | g2837.t1 | SUPERFAMILY | SSF47364 | Domain of the SRP/SRP receptor G-proteins | 308 | 390 | 5.53E-11 |
| 8 | g2837.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 407 | 627 | 1.63E-41 |
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:0006886 | intracellular protein transport | BP |
| GO:0006614 | SRP-dependent cotranslational protein targeting to membrane | BP |
| GO:0005525 | GTP binding | MF |
| GO:0005047 | signal recognition particle binding | MF |
| GO:0005785 | signal recognition particle receptor complex | CC |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K13431 (signal recognition particle receptor subunit alpha)
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.
