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.t7 isoform g4403.t7 1996600 1998984
chr_2 g4403 g4403.t7 exon g4403.t7.exon1 1996600 1997095
chr_2 g4403 g4403.t7 TSS g4403.t7 1996936 1996936
chr_2 g4403 g4403.t7 cds g4403.t7.CDS1 1996980 1997095
chr_2 g4403 g4403.t7 exon g4403.t7.exon2 1997165 1997280
chr_2 g4403 g4403.t7 cds g4403.t7.CDS2 1997165 1997280
chr_2 g4403 g4403.t7 exon g4403.t7.exon3 1997342 1998117
chr_2 g4403 g4403.t7 cds g4403.t7.CDS3 1997342 1998117
chr_2 g4403 g4403.t7 exon g4403.t7.exon4 1998170 1998984
chr_2 g4403 g4403.t7 cds g4403.t7.CDS4 1998170 1998373
chr_2 g4403 g4403.t7 TTS g4403.t7 1998976 1998976

Sequences

>g4403.t7 Gene=g4403 Length=2203
ATGGAAAATTCTTCTTTGCCGCCTCTTTTTGACGACAATATGCAAAATGTGGATATCAGT
TCACCCAATGAAGTTGAGCAATCATTATTTGAGTCAGCGATGGAAGAGGTAATTCAAATT
TTTTAAAAAAATTGCGATGAGAAAAATTATTAATCATCATTTTCTCATTTGTTAAATTTC
TTATCGCAAAACAGTTATTATTTTATATATGACGCTTTATCGGTTTCGAGCTGCACTTTT
ACAATTAATGATTTGTTTCTATAATTCGCCTTTATTGAATCAACAAAAATATGCGGGTGA
TGAATGTAATACATTTTTTTTTGATTTAGGAAAATGATCTCATTCAAACACCAACTTTGA
AAGAGAGTAATGCAGCAATTATGGAAGATGTGATAACAACATCTGATGAAAGAGAAACCA
ATGGACATTATATTGAAATTTCTGTTGAGGAGCCACAAAAAATGGGAGATGGCATGAATA
GTTATTTAGTTTACAAAGTTATAACAAAAACTAATATACCCAAGTTTTCGCGAAGACAAT
CAACTGTACTTCGAAGATTCAGTGACTTTTTGGGACTTCATGAACAACTTGTTGAACGTT
ATTTACGAGCTGGTTTTATTATTCCTCCTGCTCCATCGAAGAATATTTTAGGTGCTACAA
AAGTTAAAATGGGAACTCAACAGAATATTGAACCAGGCGCTGCCACAAATGCGCAAGAAT
GGGTAGAAAATCGTCGTGCGAGTTTGGAGAGATTTTTGAATAGAACTGCAGCTCATCCAA
CGCTTCGACATGATAGCAATTTCATTCATTTTCTTGAAAATGAACAAGATTTACCTCGTG
CAACAAACACTGCTGCTCTAAGTGGTGCTGGCGTTATGAGGCTATTTAACAAAGTTGGTG
AAACTGTGAACAAAATTACATACAAAATGGATGAAAATGATACATGGTTTGCTGATAAAA
TACAAGAGATTGATTCTCTTGATTCTCATTACCAAAAGTTGCATATTGCTGTAAAATCGC
TAGTTGCACATCGACAAGAATTAGCACACTTAACAGGAAATGTTGCTAAATCTGCAGCTA
TGCTGAGTACATGTGAGGAACATGTTGGTCTTTCAAAAGCCTTATCACAACTAGCAGATG
TTGAGGAAAAAATTGAAATATTAAGGTCTGAACAGTCAAATTCAGATTTTTATATTCTAT
CAGAGATGATTAAAGATTACATTGGCTTGCTTGGTGCTATCAAAGATGTTTTTCATGAAC
GTGTTAAAGTTTTTCAAAATTGGCAACATGCTCAGACTCAGTTAACAAAGAAACGAGAGA
ATAAAGCAAAATTGGAATTGAATCAACGCAATGATAAAATTGATCAAGCTCAGAAAGAAG
TTGAAGAGTGGGAAACAAAAGTGCAACGTTGTCAGAAAGAATTTGAAGACATTTCTGCAG
AAATAAAACGTGAAGTTGAACGCTTTGAAATAAATAGAGCAAAGGACTTTAAGTCGACTA
TTATCAAATATTTACAAGATCAGATGGCTCATCAGCAGCAAATTATGAAATATTGGGAAA
ATTATATGCCTGCGGCAAAAGAAATTGCATGAAACACAGCAACTGTTTTAAAGAAATCTG
ATAAGGTTCATCTTATTGTGTGAGCTTTTTTTGCTTTTATAACAGCAGGTTAAAATATTT
TTTCGTACTATCTACACATTTTTTTGACAATTTTCCTTCTCTCAGTTTTTCATGCTGCTG
AAAAACAAAATATCATGTATGTCCTATATTTGTTTACGTCAACCTCAATGATCTTTTCTT
AAAAAGATTATATTTTATGAAATTAGTTTAATCGATCAACTATTGATTCGCTATTGCTTT
TCATTCATTATTTTTTGATACGTATGTGTATATCACCCAAAAAAACACACGTAACATTGT
ATAATTTATACATAAAACTTTTTTATACATCAATAATGTTTAAACATTCCGAAGAAATAT
TTGTTAAAATAATGATAACGTCATTATAACTTTATATATTGTATGAATGTATTCATATTA
TGATTTTACATAAATCAATTTCATATTGATATATTTTGAAGATGAGAGAAAAAATAAGAA
ATCATTTTGAATATTATAAAAAAAGGTTTATTCTTTATATTATTAGAGGATAATGTTTAT
AAATCACGAATAAATTATTTAATCACTTTATTCGAATATGCTC

>g4403.t7 Gene=g4403 Length=403
MEDVITTSDERETNGHYIEISVEEPQKMGDGMNSYLVYKVITKTNIPKFSRRQSTVLRRF
SDFLGLHEQLVERYLRAGFIIPPAPSKNILGATKVKMGTQQNIEPGAATNAQEWVENRRA
SLERFLNRTAAHPTLRHDSNFIHFLENEQDLPRATNTAALSGAGVMRLFNKVGETVNKIT
YKMDENDTWFADKIQEIDSLDSHYQKLHIAVKSLVAHRQELAHLTGNVAKSAAMLSTCEE
HVGLSKALSQLADVEEKIEILRSEQSNSDFYILSEMIKDYIGLLGAIKDVFHERVKVFQN
WQHAQTQLTKKRENKAKLELNQRNDKIDQAQKEVEEWETKVQRCQKEFEDISAEIKREVE
RFEINRAKDFKSTIIKYLQDQMAHQQQIMKYWENYMPAAKEIA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4403.t7 CDD cd06859 PX_SNX1_2_like 18 148 4.13037E-57
12 g4403.t7 CDD cd07623 BAR_SNX1_2 177 400 3.75487E-125
9 g4403.t7 Coils Coil Coil 244 264 -
10 g4403.t7 Coils Coil Coil 313 361 -
7 g4403.t7 Gene3D G3DSA:3.30.1520.10 PX domain 9 158 6.9E-41
8 g4403.t7 Gene3D G3DSA:1.20.1270.60 Arfaptin 181 403 6.4E-70
3 g4403.t7 PANTHER PTHR10555 SORTING NEXIN 9 403 1.0E-137
4 g4403.t7 PANTHER PTHR10555:SF129 SORTING NEXIN-1 9 403 1.0E-137
2 g4403.t7 Pfam PF00787 PX domain 48 147 1.0E-19
1 g4403.t7 Pfam PF09325 Vps5 C terminal like 166 397 1.2E-84
14 g4403.t7 ProSiteProfiles PS50195 PX domain profile. 16 152 18.636
13 g4403.t7 SMART SM00312 PX_2 15 148 2.3E-26
6 g4403.t7 SUPERFAMILY SSF64268 PX domain 13 148 8.37E-29
5 g4403.t7 SUPERFAMILY SSF103657 BAR/IMD domain-like 187 397 4.71E-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

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