Gene loci information

Transcript annotation

  • This transcript has been annotated as Sorting nexin-2.

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_2 g4403 g4403.t5 TSS g4403.t5 1996546 1996546
chr_2 g4403 g4403.t5 isoform g4403.t5 1996600 1998113
chr_2 g4403 g4403.t5 exon g4403.t5.exon1 1996600 1996707
chr_2 g4403 g4403.t5 exon g4403.t5.exon2 1996929 1997095
chr_2 g4403 g4403.t5 exon g4403.t5.exon3 1997165 1997258
chr_2 g4403 g4403.t5 exon g4403.t5.exon4 1997311 1998113
chr_2 g4403 g4403.t5 cds g4403.t5.CDS1 1997398 1998111
chr_2 g4403 g4403.t5 TTS g4403.t5 1998976 1998976

Sequences

>g4403.t5 Gene=g4403 Length=1172
ATGGAAAATTCTTCTTTGCCGCCTCTTTTTGACGACAATATGCAAAATGTGGATATCAGT
TCACCCAATGAAGTTGAGCAATCATTATTTGAGTCAGCGATGGAAGAGGAAAATGATCTC
ATTCAAACACCAACTTTGAAAGAGAGTAATGCAGCAATTATGGAAGATGTGATAACAACA
TCTGATGAAAGAGAAACCAATGGACATTATATTGAAATTTCTGTTGAGGAGCCACAAAAA
ATGGGAGATGGCATGAATAGTTATTTAGTTTACAAAGTTATAACAAAAACTAATATACCC
AAGTTTTCGCGAAGACAATCAACTGTACTTCGAAGATTCAGTGACTTTTTGGGACTTCAT
GAACAACTTCATTTAATTATCAAGATATTCATTTTTTAAGGTTTTATTATTCCTCCTGCT
CCATCGAAGAATATTTTAGGTGCTACAAAAGTTAAAATGGGAACTCAACAGAATATTGAA
CCAGGCGCTGCCACAAATGCGCAAGAATGGGTAGAAAATCGTCGTGCGAGTTTGGAGAGA
TTTTTGAATAGAACTGCAGCTCATCCAACGCTTCGACATGATAGCAATTTCATTCATTTT
CTTGAAAATGAACAAGATTTACCTCGTGCAACAAACACTGCTGCTCTAAGTGGTGCTGGC
GTTATGAGGCTATTTAACAAAGTTGGTGAAACTGTGAACAAAATTACATACAAAATGGAT
GAAAATGATACATGGTTTGCTGATAAAATACAAGAGATTGATTCTCTTGATTCTCATTAC
CAAAAGTTGCATATTGCTGTAAAATCGCTAGTTGCACATCGACAAGAATTAGCACACTTA
ACAGGAAATGTTGCTAAATCTGCAGCTATGCTGAGTACATGTGAGGAACATGTTGGTCTT
TCAAAAGCCTTATCACAACTAGCAGATGTTGAGGAAAAAATTGAAATATTAAGGTCTGAA
CAGTCAAATTCAGATTTTTATATTCTATCAGAGATGATTAAAGATTACATTGGCTTGCTT
GGTGCTATCAAAGATGTTTTTCATGAACGTGTTAAAGTTTTTCAAAATTGGCAACATGCT
CAGACTCAGTTAACAAAGAAACGAGAGAATAAAGCAAAATTGGAATTGAATCAACGCAAT
GATAAAATTGATCAAGCTCAGAAAGAAGTTGA

>g4403.t5 Gene=g4403 Length=238
MGTQQNIEPGAATNAQEWVENRRASLERFLNRTAAHPTLRHDSNFIHFLENEQDLPRATN
TAALSGAGVMRLFNKVGETVNKITYKMDENDTWFADKIQEIDSLDSHYQKLHIAVKSLVA
HRQELAHLTGNVAKSAAMLSTCEEHVGLSKALSQLADVEEKIEILRSEQSNSDFYILSEM
IKDYIGLLGAIKDVFHERVKVFQNWQHAQTQLTKKRENKAKLELNQRNDKIDQAQKEV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4403.t5 Coils Coil Coil 148 168 -
8 g4403.t5 Coils Coil Coil 217 237 -
6 g4403.t5 Gene3D G3DSA:3.30.1520.10 PX domain 2 62 7.0E-13
7 g4403.t5 Gene3D G3DSA:1.20.1270.60 Arfaptin 85 238 7.5E-44
3 g4403.t5 PANTHER PTHR10555 SORTING NEXIN 14 238 4.6E-76
4 g4403.t5 PANTHER PTHR10555:SF129 SORTING NEXIN-1 14 238 4.6E-76
2 g4403.t5 Pfam PF00787 PX domain 16 51 3.6E-7
1 g4403.t5 Pfam PF09325 Vps5 C terminal like 70 238 1.5E-58
5 g4403.t5 SUPERFAMILY SSF64268 PX domain 14 52 4.45E-8

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:0030904 retromer complex CC
GO:0042147 retrograde transport, endosome to Golgi BP
GO:0035091 phosphatidylinositol binding 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