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.t9 TSS g4403.t9 1996936 1996936
chr_2 g4403 g4403.t9 isoform g4403.t9 1997258 1998984
chr_2 g4403 g4403.t9 exon g4403.t9.exon1 1997258 1997280
chr_2 g4403 g4403.t9 exon g4403.t9.exon2 1997342 1998117
chr_2 g4403 g4403.t9 cds g4403.t9.CDS1 1997398 1998117
chr_2 g4403 g4403.t9 exon g4403.t9.exon3 1998170 1998984
chr_2 g4403 g4403.t9 cds g4403.t9.CDS2 1998170 1998373
chr_2 g4403 g4403.t9 TTS g4403.t9 1998976 1998976

Sequences

>g4403.t9 Gene=g4403 Length=1614
TGTTGAACGTTATTTACGAGCTGGTTTTATTATTCCTCCTGCTCCATCGAAGAATATTTT
AGGTGCTACAAAAGTTAAAATGGGAACTCAACAGAATATTGAACCAGGCGCTGCCACAAA
TGCGCAAGAATGGGTAGAAAATCGTCGTGCGAGTTTGGAGAGATTTTTGAATAGAACTGC
AGCTCATCCAACGCTTCGACATGATAGCAATTTCATTCATTTTCTTGAAAATGAACAAGA
TTTACCTCGTGCAACAAACACTGCTGCTCTAAGTGGTGCTGGCGTTATGAGGCTATTTAA
CAAAGTTGGTGAAACTGTGAACAAAATTACATACAAAATGGATGAAAATGATACATGGTT
TGCTGATAAAATACAAGAGATTGATTCTCTTGATTCTCATTACCAAAAGTTGCATATTGC
TGTAAAATCGCTAGTTGCACATCGACAAGAATTAGCACACTTAACAGGAAATGTTGCTAA
ATCTGCAGCTATGCTGAGTACATGTGAGGAACATGTTGGTCTTTCAAAAGCCTTATCACA
ACTAGCAGATGTTGAGGAAAAAATTGAAATATTAAGGTCTGAACAGTCAAATTCAGATTT
TTATATTCTATCAGAGATGATTAAAGATTACATTGGCTTGCTTGGTGCTATCAAAGATGT
TTTTCATGAACGTGTTAAAGTTTTTCAAAATTGGCAACATGCTCAGACTCAGTTAACAAA
GAAACGAGAGAATAAAGCAAAATTGGAATTGAATCAACGCAATGATAAAATTGATCAAGC
TCAGAAAGAAGTTGAAGAGTGGGAAACAAAAGTGCAACGTTGTCAGAAAGAATTTGAAGA
CATTTCTGCAGAAATAAAACGTGAAGTTGAACGCTTTGAAATAAATAGAGCAAAGGACTT
TAAGTCGACTATTATCAAATATTTACAAGATCAGATGGCTCATCAGCAGCAAATTATGAA
ATATTGGGAAAATTATATGCCTGCGGCAAAAGAAATTGCATGAAACACAGCAACTGTTTT
AAAGAAATCTGATAAGGTTCATCTTATTGTGTGAGCTTTTTTTGCTTTTATAACAGCAGG
TTAAAATATTTTTTCGTACTATCTACACATTTTTTTGACAATTTTCCTTCTCTCAGTTTT
TCATGCTGCTGAAAAACAAAATATCATGTATGTCCTATATTTGTTTACGTCAACCTCAAT
GATCTTTTCTTAAAAAGATTATATTTTATGAAATTAGTTTAATCGATCAACTATTGATTC
GCTATTGCTTTTCATTCATTATTTTTTGATACGTATGTGTATATCACCCAAAAAAACACA
CGTAACATTGTATAATTTATACATAAAACTTTTTTATACATCAATAATGTTTAAACATTC
CGAAGAAATATTTGTTAAAATAATGATAACGTCATTATAACTTTATATATTGTATGAATG
TATTCATATTATGATTTTACATAAATCAATTTCATATTGATATATTTTGAAGATGAGAGA
AAAAATAAGAAATCATTTTGAATATTATAAAAAAAGGTTTATTCTTTATATTATTAGAGG
ATAATGTTTATAAATCACGAATAAATTATTTAATCACTTTATTCGAATATGCTC

>g4403.t9 Gene=g4403 Length=307
MGTQQNIEPGAATNAQEWVENRRASLERFLNRTAAHPTLRHDSNFIHFLENEQDLPRATN
TAALSGAGVMRLFNKVGETVNKITYKMDENDTWFADKIQEIDSLDSHYQKLHIAVKSLVA
HRQELAHLTGNVAKSAAMLSTCEEHVGLSKALSQLADVEEKIEILRSEQSNSDFYILSEM
IKDYIGLLGAIKDVFHERVKVFQNWQHAQTQLTKKRENKAKLELNQRNDKIDQAQKEVEE
WETKVQRCQKEFEDISAEIKREVERFEINRAKDFKSTIIKYLQDQMAHQQQIMKYWENYM
PAAKEIA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4403.t9 CDD cd07623 BAR_SNX1_2 81 304 3.23E-122
10 g4403.t9 Coils Coil Coil 148 168 -
9 g4403.t9 Coils Coil Coil 217 265 -
7 g4403.t9 Gene3D G3DSA:3.30.1520.10 PX domain 2 62 1.1E-12
8 g4403.t9 Gene3D G3DSA:1.20.1270.60 Arfaptin 85 307 2.9E-70
3 g4403.t9 PANTHER PTHR10555 SORTING NEXIN 14 307 1.2E-101
4 g4403.t9 PANTHER PTHR10555:SF129 SORTING NEXIN-1 14 307 1.2E-101
2 g4403.t9 Pfam PF00787 PX domain 16 51 5.3E-7
1 g4403.t9 Pfam PF09325 Vps5 C terminal like 70 301 5.2E-85
6 g4403.t9 SUPERFAMILY SSF64268 PX domain 14 52 6.54E-8
5 g4403.t9 SUPERFAMILY SSF103657 BAR/IMD domain-like 91 301 1.86E-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