Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Signal recognition particle receptor subunit beta.

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 g2470 g2470.t1 TTS g2470.t1 18122923 18122923
chr_3 g2470 g2470.t1 isoform g2470.t1 18122965 18123802
chr_3 g2470 g2470.t1 exon g2470.t1.exon1 18122965 18123154
chr_3 g2470 g2470.t1 cds g2470.t1.CDS1 18122965 18123154
chr_3 g2470 g2470.t1 exon g2470.t1.exon2 18123216 18123651
chr_3 g2470 g2470.t1 cds g2470.t1.CDS2 18123216 18123651
chr_3 g2470 g2470.t1 exon g2470.t1.exon3 18123709 18123802
chr_3 g2470 g2470.t1 cds g2470.t1.CDS3 18123709 18123802
chr_3 g2470 g2470.t1 TSS g2470.t1 18123878 18123878

Sequences

>g2470.t1 Gene=g2470 Length=720
ATGGATAAAGAGACAAGAAAAGAGCCAATTAGGCTCAGTGAAATCAATTTTACTCCCATT
CTCATTGCATTTGCTGTAGTTTTCTTAACATTAGTTATCATCTATTTAATCAAAAAACGT
AGTCCAAGAAGAACAGACATTTTACTAGCTGGCTTATGTGATTCAGGAAAGACTCTTTTG
TATTCATTGCTACTCAATGGAAATGAAGTCGAGACATTTACTTCATTAAAAGAAAATTGT
GGAATTTTTCAAATTGAAGATAGCAAATCACTTCGTATTGTTGATCTTCCAGGCCATGAA
AGACTTCGTTTGAGATTACTGGAAAATTATAAAAATTCAACAAAAGCCATCATCTACGTC
GTTGATTCAACTACTGTTCAAAAAGAGATTCGTGATGTTGCAGATTTCTTATACACATTA
CTCGCTGATAAAGCACTTTCATCATTGAACGTTTTAATTTTGTGTAACAAGCAAGATGAG
ACCATGGCTAAAGGAAAACAAGTGGTTGAACAATTACTTGAAAAAGAAATTAATGTAATT
CGAAAGACAAGAACAAGCCAATTGCAGTCAGTTGATAATTCATCAGATAAAACAATGTAC
CTAGGAAAAAGCGACAAAGACTTTGATTTTTCACAAATCTCACAGAAAATTTCATTTGCC
GAATCATCAGCAAAGAATAAAGATATTGAACAAATAATTAGCTTCATAAAGGCTCTGTAA

>g2470.t1 Gene=g2470 Length=239
MDKETRKEPIRLSEINFTPILIAFAVVFLTLVIIYLIKKRSPRRTDILLAGLCDSGKTLL
YSLLLNGNEVETFTSLKENCGIFQIEDSKSLRIVDLPGHERLRLRLLENYKNSTKAIIYV
VDSTTVQKEIRDVADFLYTLLADKALSSLNVLILCNKQDETMAKGKQVVEQLLEKEINVI
RKTRTSQLQSVDNSSDKTMYLGKSDKDFDFSQISQKISFAESSAKNKDIEQIISFIKAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2470.t1 CDD cd04105 SR_beta 47 236 1.60122E-66
5 g2470.t1 Gene3D G3DSA:3.40.50.300 - 38 239 7.8E-64
2 g2470.t1 PANTHER PTHR11485:SF34 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT BETA 10 237 5.6E-56
3 g2470.t1 PANTHER PTHR11485 TRANSFERRIN 10 237 5.6E-56
1 g2470.t1 Pfam PF09439 Signal recognition particle receptor beta subunit 44 216 2.8E-52
7 g2470.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
8 g2470.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 37 -
6 g2470.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 38 239 -
13 g2470.t1 ProSiteProfiles PS51417 small GTPase Arf family profile. 38 217 8.565
12 g2470.t1 SMART SM00178 sar_sub_1 24 233 0.0095
11 g2470.t1 SMART SM00177 arf_sub_2 25 214 0.0082
4 g2470.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 47 233 8.33E-24
10 g2470.t1 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

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.

Raw TPM values