Gene loci information

Transcript annotation

  • This transcript has been annotated as Sorting nexin-3.

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_4 g15754 g15754.t2 isoform g15754.t2 6667918 6669713
chr_4 g15754 g15754.t2 exon g15754.t2.exon1 6667918 6667948
chr_4 g15754 g15754.t2 TTS g15754.t2 6667930 6667930
chr_4 g15754 g15754.t2 exon g15754.t2.exon2 6668552 6669473
chr_4 g15754 g15754.t2 cds g15754.t2.CDS1 6669147 6669473
chr_4 g15754 g15754.t2 exon g15754.t2.exon3 6669534 6669713
chr_4 g15754 g15754.t2 cds g15754.t2.CDS2 6669534 6669713
chr_4 g15754 g15754.t2 TSS g15754.t2 6669650 6669650

Sequences

>g15754.t2 Gene=g15754 Length=1133
ATGAATTCACCCGAAGAAAATTTCGAGAACAATTCAATATCTCGATTAGCCACAAAAAAG
CAAAGTTTAGATGACATGTATTCAGTGCCAGCTAATTTCTTAGAAATTGATGTTGTCAAT
CCACAGACAAAAATTATAGCTGGAAAAAAGAAGTATACAGATTATGAGATTCGTATGAAG
ACTAATCTTCCAGTTTTCAAAATAAAAGAATCCAGCGTTCGTCGTCGTTATTCAGACTTT
GAATGGCTTCGTAATGAACTTGAACGTGACAGTAAAATTGTTGTGCCACCTTTACCATCA
AAAGCATGGAAAAGGCAACTTCCATTTTGGAGTGATGATGGATTATTTGATGAGAATTTT
ATTGAAGAAAGAAGAAAAGGACTAGAAATTTTTGTTAACAAAATCGCAGGGCATCCGCTT
GCACAGAATGAGAGATGTTTGCATATGTTCTTACAAGAACCTGTTATTGATCGAGGTTAC
ACACCTGGTAAAGTAAGAAATGCTTAAAGAGAAGGTTTTTAAAGATTATTGCTGATTGGA
AAGGAATTTTTTAAAATGTTTTACTTTAGAAATTGTAGATTTAGCCAATGTCTACAGATT
TTCTTAAACTTAATGTGAGATTATATATGAGCATTTTTATCAAATAATTTAACTTTCATT
CAAATTTCATTTATTATTTTTAGACATGGTTTGATATGTCTTGACAAAAAGTTGTACTAT
TTTTTAATTAAATTTATTTTATTCCGTACAATAATTTAAATTACAGACAGCTGATTATAA
TAATTTTCATTTCATCACTATTGACTTTTTAGAATTTAAAAGTTTTCTCAGCTCAAAAAT
ATTTTAAACACTTCCATAAAAATTAAATTATAAAATAAAAATATCCTTTCACTAAAACCT
TAAAAAGCCAACAAAACAAAATAAAGTGCTGCAATTAATTTGAACGATTTAAATATTTTT
TAAGGCTCAGTTAACAATAAGTCAACAGCTCAAGCGTGAATGTTTATCTTGCTATTATTT
TAAAATTTCTCTTTATTAGAATTATTATTATTATCCTATAAATGAATGTATGTAAAAATG
CAATGTTATTTGAAATATAAAATAAAAATGTATGAATGATTAAAATTTTGTCT

>g15754.t2 Gene=g15754 Length=168
MNSPEENFENNSISRLATKKQSLDDMYSVPANFLEIDVVNPQTKIIAGKKKYTDYEIRMK
TNLPVFKIKESSVRRRYSDFEWLRNELERDSKIVVPPLPSKAWKRQLPFWSDDGLFDENF
IEERRKGLEIFVNKIAGHPLAQNERCLHMFLQEPVIDRGYTPGKVRNA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g15754.t2 CDD cd06894 PX_SNX3_like 33 156 0.000
6 g15754.t2 Gene3D G3DSA:3.30.1520.10 PX domain 27 165 0.000
2 g15754.t2 PANTHER PTHR45963:SF3 SORTING NEXIN-12 14 167 0.000
3 g15754.t2 PANTHER PTHR45963 RE52028P 14 167 0.000
1 g15754.t2 Pfam PF00787 PX domain 65 153 0.000
7 g15754.t2 ProSiteProfiles PS50195 PX domain profile. 33 157 17.978
5 g15754.t2 SMART SM00312 PX_2 31 154 0.000
4 g15754.t2 SUPERFAMILY SSF64268 PX domain 31 154 0.000

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:0035091 phosphatidylinositol binding MF

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. There were no conditions that were differentially expressed