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.t3 TTS g2470.t3 18122923 18122923
chr_3 g2470 g2470.t3 isoform g2470.t3 18122965 18123802
chr_3 g2470 g2470.t3 exon g2470.t3.exon1 18122965 18123154
chr_3 g2470 g2470.t3 cds g2470.t3.CDS1 18123152 18123154
chr_3 g2470 g2470.t3 exon g2470.t3.exon2 18123245 18123651
chr_3 g2470 g2470.t3 cds g2470.t3.CDS2 18123245 18123651
chr_3 g2470 g2470.t3 exon g2470.t3.exon3 18123709 18123802
chr_3 g2470 g2470.t3 cds g2470.t3.CDS3 18123709 18123802
chr_3 g2470 g2470.t3 TSS g2470.t3 18123878 18123878

Sequences

>g2470.t3 Gene=g2470 Length=691
ATGGATAAAGAGACAAGAAAAGAGCCAATTAGGCTCAGTGAAATCAATTTTACTCCCATT
CTCATTGCATTTGCTGTAGTTTTCTTAACATTAGTTATCATCTATTTAATCAAAAAACGT
AGTCCAAGAAGAACAGACATTTTACTAGCTGGCTTATGTGATTCAGGAAAGACTCTTTTG
TATTCATTGCTACTCAATGGAAATGAAGTCGAGACATTTACTTCATTAAAAGAAAATTGT
GGAATTTTTCAAATTGAAGATAGCAAATCACTTCGTATTGTTGATCTTCCAGGCCATGAA
AGACTTCGTTTGAGATTACTGGAAAATTATAAAAATTCAACAAAAGCCATCATCTACGTC
GTTGATTCAACTACTGTTCAAAAAGAGATTCGTGATGTTGCAGATTTCTTATACACATTA
CTCGCTGATAAAGCACTTTCATCATTGAACGTTTTAATTTTGTGTAACAAGCAAGATGAG
ACCATGGCTAAAGGAAAACAATAATGTAATTCGAAAGACAAGAACAAGCCAATTGCAGTC
AGTTGATAATTCATCAGATAAAACAATGTACCTAGGAAAAAGCGACAAAGACTTTGATTT
TTCACAAATCTCACAGAAAATTTCATTTGCCGAATCATCAGCAAAGAATAAAGATATTGA
ACAAATAATTAGCTTCATAAAGGCTCTGTAA

>g2470.t3 Gene=g2470 Length=167
MDKETRKEPIRLSEINFTPILIAFAVVFLTLVIIYLIKKRSPRRTDILLAGLCDSGKTLL
YSLLLNGNEVETFTSLKENCGIFQIEDSKSLRIVDLPGHERLRLRLLENYKNSTKAIIYV
VDSTTVQKEIRDVADFLYTLLADKALSSLNVLILCNKQDETMAKGKQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2470.t3 Gene3D G3DSA:3.40.50.300 - 38 167 1.5E-43
2 g2470.t3 PANTHER PTHR11485:SF34 SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT BETA 10 166 5.5E-42
3 g2470.t3 PANTHER PTHR11485 TRANSFERRIN 10 166 5.5E-42
1 g2470.t3 Pfam PF09439 Signal recognition particle receptor beta subunit 44 165 9.6E-37
8 g2470.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
9 g2470.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 37 -
7 g2470.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 38 167 -
5 g2470.t3 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 42 163 3.03E-21
4 g2470.t3 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

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. There were no conditions that were differentially expressed