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.t6 TSS g2837.t6 20504191 20504191
chr_3 g2837 g2837.t6 isoform g2837.t6 20504264 20506177
chr_3 g2837 g2837.t6 exon g2837.t6.exon1 20504264 20505606
chr_3 g2837 g2837.t6 cds g2837.t6.CDS1 20504767 20505606
chr_3 g2837 g2837.t6 exon g2837.t6.exon2 20505673 20506177
chr_3 g2837 g2837.t6 cds g2837.t6.CDS2 20505673 20506176
chr_3 g2837 g2837.t6 TTS g2837.t6 20506475 20506475

Sequences

>g2837.t6 Gene=g2837 Length=1848
ATGCTCGATTTGTTTACGATTTTCACTAAAGGAGGCATAGTTCTCTGGTGTTTCCGAAAT
ATAAATGAGCCTTTTGCACCATCAATCAATGCCTTGATCAAAAATATATTGATGCAGGTG
AGTAAATAAATTTATTTTGACAAAGAAACCATAATAACTTTCACTTTTAAAAAAATTGGC
TTAAATTAATGTTTTTTCCTAATATAATATAATTTTAGGAGCGTGGAGGAAGCAACTCTT
ATGAGCACAACAACTTGACTCTTCAATATAAGCTCGATAATGAGTTTGAGTTGATATTCG
TTGTTGCCTTTCAGAAGATTTTGCAACTCGCTTACATTGACAAGTTTCTATCAGACATTC
ATTTAGAATTTCGCGATAAATATAAGAATGAATTGACATCACAGGGTAGAGAATTTTACA
ACTTTAATTTGAGCGATGAATTCAAGAGAATATTAAAAGAAGCAGAGGCATGGGGTCAAG
TGCAAAAAAGCATTCCTCGTACCATGAGAACCTTCGATGAATCACACAAGTCAAAAAAGA
CTGTTGATTCTATGATTGTTCGAAAAAGTGGTGACGATAAGTCCAATGTAAATACTAATA
AAAAATCTGTCAAAATTGTTGAAACTGAAAAAGTCAATGCCAAGAATGATGATTATGATG
ATATAAATGGAAATGCGGACAATGAGATTGCCTTGGCACGCAAAAAACTTGCAGATAAGT
TTACTAAAAAAAGTCCAGCTGATAAGAAGAAATCACCAAAATCATCATCATCATCTGAGA
AGAAAAAGAAGACAGATCGTGTTTGGGAATTGAATGGAAATTCAAAAGATGCAATAACAC
TCGATCGTTCAAAAGATCGACCTGAAGATATAAAAAGTGACTTTACACATTTGGATAAAA
TGGTTGGTCAATCAATTGGTAATATAAAAGACATTGAAATAGAGGAAGAATCATCTGAAG
AAGAAGATTCAGATGAATATGAAGAAAAAGAAACAAAGTCACAAGCTAAGAAAGCATCAC
GTAGTGGAGGCATGTTGTCAATGTTTAAAGGACTTGTTGGATCAAAATCAATTACAATTG
AAGATATGCAACCAGCTCTTGATAAATTGAGAGATCATTTGATTGCAAAAAATGTTGCTA
CTGATATATCGCAAAAATTGTGTGCTTCTGTTGCTGCAAAATTGGAGGGAAAAGTTTTGG
GTACATTTGATACAATTGCAGCAACTGTTAAAACTACTTTGAATGATTCTTTGGTTCAAA
TTCTTTCACCAAAACGACGTATTGACATTCTTCGTGATTGCTTAGAGGCAAAAAGAAATA
ATAGGCCATATGTTATGACATTCTGTGGTGTCAATGGTGTAGGCAAATCAACAAATTTGG
CAAAAATCTGTTTCTGGTTGATTGAGAATAACTTCAATGTATTGATTGCAGCTTGTGACA
CTTTTCGTGCGGGTGCTGTTGAACAGTTGCGCACACATACTCGTCATTTGAATGCACTTC
ATCCAAAAGAAAAGCATGGAGGTCGTGAGATGGTTGAGTTATATGAAAAAGGATATGGCA
AAGATGCAGCAGGAATAGCAATGGAAGCGATTCGTTATGCTAAAGAAGCAGGAATTGATG
TTGTTCTTGTTGATACTGCTGGTCGAATGCAAGACAATGAACCTTTGATGCGCGCACTTG
CTAAACTGATCAAAATTAATGAGCCTGATTTGGTATTATTCGTTGGTGAGGCTCTTGTTG
GAAATGAAGCTGTCGATCAATTGGTGAAATTTAATCAAGCTCTTGCTGATCATTCTTCAA
TGGAAAATCCTCATGTTATTGATGGAATCGTTTTAACTAAATTTGACA

>g2837.t6 Gene=g2837 Length=448
MRTFDESHKSKKTVDSMIVRKSGDDKSNVNTNKKSVKIVETEKVNAKNDDYDDINGNADN
EIALARKKLADKFTKKSPADKKKSPKSSSSSEKKKKTDRVWELNGNSKDAITLDRSKDRP
EDIKSDFTHLDKMVGQSIGNIKDIEIEEESSEEEDSDEYEEKETKSQAKKASRSGGMLSM
FKGLVGSKSITIEDMQPALDKLRDHLIAKNVATDISQKLCASVAAKLEGKVLGTFDTIAA
TVKTTLNDSLVQILSPKRRIDILRDCLEAKRNNRPYVMTFCGVNGVGKSTNLAKICFWLI
ENNFNVLIAACDTFRAGAVEQLRTHTRHLNALHPKEKHGGREMVELYEKGYGKDAAGIAM
EAIRYAKEAGIDVVLVDTAGRMQDNEPLMRALAKLIKINEPDLVLFVGEALVGNEAVDQL
VKFNQALADHSSMENPHVIDGIVLTKFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g2837.t6 CDD cd17876 SRalpha_C 276 448 1.16905E-112
17 g2837.t6 Gene3D G3DSA:1.20.120.140 - 142 256 4.1E-23
16 g2837.t6 Gene3D G3DSA:3.40.50.300 - 259 448 1.3E-73
14 g2837.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 35 -
12 g2837.t6 MobiDBLite mobidb-lite consensus disorder prediction 71 106 -
15 g2837.t6 MobiDBLite mobidb-lite consensus disorder prediction 71 103 -
13 g2837.t6 MobiDBLite mobidb-lite consensus disorder prediction 138 173 -
11 g2837.t6 MobiDBLite mobidb-lite consensus disorder prediction 146 160 -
4 g2837.t6 PANTHER PTHR43134:SF1 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA 17 448 1.2E-158
5 g2837.t6 PANTHER PTHR43134 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA 17 448 1.2E-158
1 g2837.t6 Pfam PF04086 Signal recognition particle, alpha subunit, N-terminal 2 148 2.5E-8
2 g2837.t6 Pfam PF02881 SRP54-type protein, helical bundle domain 175 246 4.8E-9
3 g2837.t6 Pfam PF00448 SRP54-type protein, GTPase domain 276 448 8.6E-36
8 g2837.t6 SMART SM00963 SRP54_N_2 180 254 3.8E-6
9 g2837.t6 SMART SM00382 AAA_5 274 427 9.0E-8
10 g2837.t6 SMART SM00962 SRP54_3 275 448 4.5E-39
6 g2837.t6 SUPERFAMILY SSF47364 Domain of the SRP/SRP receptor G-proteins 174 256 3.29E-11
7 g2837.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 273 448 4.35E-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