Gene loci information

Transcript annotation

  • This transcript has been annotated as Signal recognition particle receptor subunit alpha-like protein.

Parent gene

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.t4 TSS g2837.t4 20504191 20504191
chr_3 g2837 g2837.t4 isoform g2837.t4 20504264 20505590
chr_3 g2837 g2837.t4 exon g2837.t4.exon1 20504264 20504380
chr_3 g2837 g2837.t4 cds g2837.t4.CDS1 20504264 20504380
chr_3 g2837 g2837.t4 exon g2837.t4.exon2 20504482 20505590
chr_3 g2837 g2837.t4 cds g2837.t4.CDS2 20504482 20505588
chr_3 g2837 g2837.t4 TTS g2837.t4 20506475 20506475

Sequences

>g2837.t4 Gene=g2837 Length=1226
ATGCTCGATTTGTTTACGATTTTCACTAAAGGAGGCATAGTTCTCTGGTGTTTCCGAAAT
ATAAATGAGCCTTTTGCACCATCAATCAATGCCTTGATCAAAAATATATTGATGCAGGAG
CGTGGAGGAAGCAACTCTTATGAGCACAACAACTTGACTCTTCAATATAAGCTCGATAAT
GAGTTTGAGTTGATATTCGTTGTTGCCTTTCAGAAGATTTTGCAACTCGCTTACATTGAC
AAGTTTCTATCAGACATTCATTTAGAATTTCGCGATAAATATAAGAATGAATTGACATCA
CAGGGTAGAGAATTTTACAACTTTAATTTGAGCGATGAATTCAAGAGAATATTAAAAGAA
GCAGAGGCATGGGGTCAAGTGCAAAAAAGCATTCCTCGTACCATGAGAACCTTCGATGAA
TCACACAAGTCAAAAAAGACTGTTGATTCTATGATTGTTCGAAAAAGTGGTGACGATAAG
TCCAATGTAAATACTAATAAAAAATCTGTCAAAATTGTTGAAACTGAAAAAGTCAATGCC
AAGAATGATGATTATGATGATATAAATGGAAATGCGGACAATGAGATTGCCTTGGCACGC
AAAAAACTTGCAGATAAGTTTACTAAAAAAAGTCCAGCTGATAAGAAGAAATCACCAAAA
TCATCATCATCATCTGAGAAGAAAAAGAAGACAGATCGTGTTTGGGAATTGAATGGAAAT
TCAAAAGATGCAATAACACTCGATCGTTCAAAAGATCGACCTGAAGATATAAAAAGTGAC
TTTACACATTTGGATAAAATGGTTGGTCAATCAATTGGTAATATAAAAGACATTGAAATA
GAGGAAGAATCATCTGAAGAAGAAGATTCAGATGAATATGAAGAAAAAGAAACAAAGTCA
CAAGCTAAGAAAGCATCACGTAGTGGAGGCATGTTGTCAATGTTTAAAGGACTTGTTGGA
TCAAAATCAATTACAATTGAAGATATGCAACCAGCTCTTGATAAATTGAGAGATCATTTG
ATTGCAAAAAATGTTGCTACTGATATATCGCAAAAATTGTGTGCTTCTGTTGCTGCAAAA
TTGGAGGGAAAAGTTTTGGGTACATTTGATACAATTGCAGCAACTGTTAAAACTACTTTG
AATGATTCTTTGGTTCAAATTCTTTCACCAAAACGACGTATTGACATTCTTCGTGATTGC
TTAGAGGCAAAAAGAAATAATAGGCC

>g2837.t4 Gene=g2837 Length=408
MLDLFTIFTKGGIVLWCFRNINEPFAPSINALIKNILMQERGGSNSYEHNNLTLQYKLDN
EFELIFVVAFQKILQLAYIDKFLSDIHLEFRDKYKNELTSQGREFYNFNLSDEFKRILKE
AEAWGQVQKSIPRTMRTFDESHKSKKTVDSMIVRKSGDDKSNVNTNKKSVKIVETEKVNA
KNDDYDDINGNADNEIALARKKLADKFTKKSPADKKKSPKSSSSSEKKKKTDRVWELNGN
SKDAITLDRSKDRPEDIKSDFTHLDKMVGQSIGNIKDIEIEEESSEEEDSDEYEEKETKS
QAKKASRSGGMLSMFKGLVGSKSITIEDMQPALDKLRDHLIAKNVATDISQKLCASVAAK
LEGKVLGTFDTIAATVKTTLNDSLVQILSPKRRIDILRDCLEAKRNNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2837.t4 CDD cd14826 SR_alpha_SRX 3 120 1.64668E-47
11 g2837.t4 Gene3D G3DSA:3.30.450.60 - 1 126 1.5E-44
12 g2837.t4 Gene3D G3DSA:1.20.120.140 - 276 390 3.5E-23
8 g2837.t4 MobiDBLite mobidb-lite consensus disorder prediction 207 237 -
10 g2837.t4 MobiDBLite mobidb-lite consensus disorder prediction 272 307 -
9 g2837.t4 MobiDBLite mobidb-lite consensus disorder prediction 280 294 -
3 g2837.t4 PANTHER PTHR43134:SF1 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA 1 408 1.1E-91
4 g2837.t4 PANTHER PTHR43134 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA 1 408 1.1E-91
1 g2837.t4 Pfam PF04086 Signal recognition particle, alpha subunit, N-terminal 29 282 1.2E-51
2 g2837.t4 Pfam PF02881 SRP54-type protein, helical bundle domain 309 380 4.1E-9
7 g2837.t4 SMART SM00963 SRP54_N_2 314 388 3.8E-6
6 g2837.t4 SUPERFAMILY SSF64356 SNARE-like 1 124 9.46E-40
5 g2837.t4 SUPERFAMILY SSF47364 Domain of the SRP/SRP receptor G-proteins 308 390 2.84E-11

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 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.

Raw TPM values