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.t5 TSS g2837.t5 20504191 20504191
chr_3 g2837 g2837.t5 isoform g2837.t5 20504264 20506177
chr_3 g2837 g2837.t5 exon g2837.t5.exon1 20504264 20504380
chr_3 g2837 g2837.t5 cds g2837.t5.CDS1 20504264 20504380
chr_3 g2837 g2837.t5 exon g2837.t5.exon2 20504482 20505606
chr_3 g2837 g2837.t5 cds g2837.t5.CDS2 20504482 20505606
chr_3 g2837 g2837.t5 exon g2837.t5.exon3 20505673 20506177
chr_3 g2837 g2837.t5 cds g2837.t5.CDS3 20505673 20506176
chr_3 g2837 g2837.t5 TTS g2837.t5 20506475 20506475

Sequences

>g2837.t5 Gene=g2837 Length=1747
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
TTTGACA

>g2837.t5 Gene=g2837 Length=582
MLDLFTIFTKGGIVLWCFRNINEPFAPSINALIKNILMQERGGSNSYEHNNLTLQYKLDN
EFELIFVVAFQKILQLAYIDKFLSDIHLEFRDKYKNELTSQGREFYNFNLSDEFKRILKE
AEAWGQVQKSIPRTMRTFDESHKSKKTVDSMIVRKSGDDKSNVNTNKKSVKIVETEKVNA
KNDDYDDINGNADNEIALARKKLADKFTKKSPADKKKSPKSSSSSEKKKKTDRVWELNGN
SKDAITLDRSKDRPEDIKSDFTHLDKMVGQSIGNIKDIEIEEESSEEEDSDEYEEKETKS
QAKKASRSGGMLSMFKGLVGSKSITIEDMQPALDKLRDHLIAKNVATDISQKLCASVAAK
LEGKVLGTFDTIAATVKTTLNDSLVQILSPKRRIDILRDCLEAKRNNRPYVMTFCGVNGV
GKSTNLAKICFWLIENNFNVLIAACDTFRAGAVEQLRTHTRHLNALHPKEKHGGREMVEL
YEKGYGKDAAGIAMEAIRYAKEAGIDVVLVDTAGRMQDNEPLMRALAKLIKINEPDLVLF
VGEALVGNEAVDQLVKFNQALADHSSMENPHVIDGIVLTKFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g2837.t5 CDD cd14826 SR_alpha_SRX 3 120 2.94183E-47
18 g2837.t5 CDD cd17876 SRalpha_C 410 582 2.9305E-112
16 g2837.t5 Gene3D G3DSA:3.30.450.60 - 1 126 2.9E-44
17 g2837.t5 Gene3D G3DSA:1.20.120.140 - 278 390 4.7E-23
15 g2837.t5 Gene3D G3DSA:3.40.50.300 - 393 582 2.2E-73
12 g2837.t5 MobiDBLite mobidb-lite consensus disorder prediction 207 237 -
14 g2837.t5 MobiDBLite mobidb-lite consensus disorder prediction 272 307 -
13 g2837.t5 MobiDBLite mobidb-lite consensus disorder prediction 280 294 -
4 g2837.t5 PANTHER PTHR43134:SF1 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA 1 582 4.1E-203
5 g2837.t5 PANTHER PTHR43134 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA 1 582 4.1E-203
1 g2837.t5 Pfam PF04086 Signal recognition particle, alpha subunit, N-terminal 29 282 6.8E-51
2 g2837.t5 Pfam PF02881 SRP54-type protein, helical bundle domain 309 380 7.0E-9
3 g2837.t5 Pfam PF00448 SRP54-type protein, GTPase domain 410 582 1.4E-35
9 g2837.t5 SMART SM00963 SRP54_N_2 314 388 3.8E-6
10 g2837.t5 SMART SM00382 AAA_5 408 561 9.0E-8
11 g2837.t5 SMART SM00962 SRP54_3 409 582 4.5E-39
7 g2837.t5 SUPERFAMILY SSF64356 SNARE-like 1 124 1.8E-39
6 g2837.t5 SUPERFAMILY SSF47364 Domain of the SRP/SRP receptor G-proteins 308 390 4.93E-11
8 g2837.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 407 582 7.04E-33

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