Gene loci information

Transcript annotation

  • This transcript has been annotated as Sorting nexin lst-4.

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_1 g13881 g13881.t1 TTS g13881.t1 33092805 33092805
chr_1 g13881 g13881.t1 isoform g13881.t1 33093310 33095130
chr_1 g13881 g13881.t1 exon g13881.t1.exon1 33093310 33093981
chr_1 g13881 g13881.t1 cds g13881.t1.CDS1 33093310 33093981
chr_1 g13881 g13881.t1 exon g13881.t1.exon2 33094038 33094978
chr_1 g13881 g13881.t1 cds g13881.t1.CDS2 33094038 33094978
chr_1 g13881 g13881.t1 exon g13881.t1.exon3 33095070 33095130
chr_1 g13881 g13881.t1 cds g13881.t1.CDS3 33095070 33095130
chr_1 g13881 g13881.t1 TSS g13881.t1 33095450 33095450

Sequences

>g13881.t1 Gene=g13881 Length=1674
ATGAAAGTTACAGTGTTATATGACTTTACCAGTGAAATCGAAAATGAGTTATCTATAATC
GCTGGGGAAATTCTCACTGTAACTGATAGAGATGTAGGTAATGGATGGTGGGAAGGGACA
AATAGTGCGGGGAAGAGAGGAATTTTTCCAGCGAGCTATGTTGAAGAGATAAAAACACCA
CAACGTCCTGTTGTACAACCAGTTGTACCTTCACAATATTATAGCAATGATATCCCTGCA
AATAATTCTTCATCCGATGATCCATGGAGTCAGTCAGCTCCAATTATTGCACCATCTTAT
AATCAACAACAGCAATCTCAACCAAATCAAAATCGATATGATTATGCTGAAGATTATGAC
TCAGATTTTGATGACGATGACAATGCATCAAGATATGCTGTTCAAACTTCATCTCATTCA
AATTATTCGAATACGCAATTGCCACCGACACCTGATGATGGTCAATCTATGGCTAGTAAT
GTAACACTTTCACGTAAAACATCGAAAATGTTTTCAAAATCATCCGATTCATATATTATG
GGCAATGCAAGCATTAATGTGTCCGAAAGTGAACAGATAAATATTTACTTAAATGACCAA
GGCCTTTACTATTGGAAACCAATTGATGGACGTTATACAGTCACAATTACATCTCCTAAA
ATGGAAAGCAAATTCAAAGGAATCAAGAAATTTATCGCTTATCAGCTTTTACCAAGTTTT
AATAATGAACCAGTATCGCGACGTTATAAAAATTTTGATTGGTTGCATGAACGTTTAGTT
GAAAAATTTTGTTTAATTCCAATACCGCCATTGCCTAATAAACAAATATCGGGTAGATAT
GAGGAGGAATTCATTGAACATCGACGTGCTCAGTTGCAAGAATTCGTTGATTATGTGTGT
CGTCATCCTGTTCTTTCAAAATGTGATGTATGGATGCATTTTATGACATGTAAAGATCAG
AAAAAATGGAAAGCCGGAAAGCGATCTGCTGAGAAGGATCCTTTGCAAGGACCATCATTT
TGTGCGGCAATACGAGTAACACCAGAAAAGGTTTTGCTACCAACATATGTTGATTCACAA
ATAGATTCTTGTAAAAATTTTACTGTTGCGATGGATGGAGCAGTCAAGATGCTCGAATCT
GCAAGTCAAGACCAAGTCAATAAATATACGAATCAATTTAAAAAAGATTATCAACGCTTA
GGTGATTGCTTTAGTGAGATGGCAAAAGCTCTTGATATCGATGAGCGACGTGCTAGCACA
GGTTATTCGTTATCACAATGTGTAGGAAATACGGCTGGTATTTTTATTTCAATTGGAAAG
TTATATGAAGAGCAAGCGAAAAAAGATTGGCAACCGTTTTGCGATAAGCTTCATGTATAT
CGAGGCATTTTGAGTTCATTTCCGGATATTTTATCGGAGCATAAAAATGCACAACAAAAG
AGAAAAGAATGTGAGAAACTCGCATTTGATCAGAAAATGTCAAATCTTCAAATTCAGGAA
GTGAATAGACGAGTTGATGTCATGACTGTCGCTTTACTCGCTGAGCAATCTCATTTTCGT
CAAGAACGTGATACACATATGAAAGAAATGATGAAAAATCTTCTTGGTGAACAGATTGCA
TTCTATCAGACAATCATTGGAAAATTACAACAAGCACAGCGCTTTTTCGATTAA

>g13881.t1 Gene=g13881 Length=557
MKVTVLYDFTSEIENELSIIAGEILTVTDRDVGNGWWEGTNSAGKRGIFPASYVEEIKTP
QRPVVQPVVPSQYYSNDIPANNSSSDDPWSQSAPIIAPSYNQQQQSQPNQNRYDYAEDYD
SDFDDDDNASRYAVQTSSHSNYSNTQLPPTPDDGQSMASNVTLSRKTSKMFSKSSDSYIM
GNASINVSESEQINIYLNDQGLYYWKPIDGRYTVTITSPKMESKFKGIKKFIAYQLLPSF
NNEPVSRRYKNFDWLHERLVEKFCLIPIPPLPNKQISGRYEEEFIEHRRAQLQEFVDYVC
RHPVLSKCDVWMHFMTCKDQKKWKAGKRSAEKDPLQGPSFCAAIRVTPEKVLLPTYVDSQ
IDSCKNFTVAMDGAVKMLESASQDQVNKYTNQFKKDYQRLGDCFSEMAKALDIDERRAST
GYSLSQCVGNTAGIFISIGKLYEEQAKKDWQPFCDKLHVYRGILSSFPDILSEHKNAQQK
RKECEKLAFDQKMSNLQIQEVNRRVDVMTVALLAEQSHFRQERDTHMKEMMKNLLGEQIA
FYQTIIGKLQQAQRFFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g13881.t1 CDD cd11763 SH3_SNX9_like 2 56 5.8205E-23
15 g13881.t1 CDD cd06862 PX_SNX9_18_like 212 335 1.46975E-74
16 g13881.t1 CDD cd07626 BAR_SNX9_like 357 556 2.75451E-83
12 g13881.t1 Gene3D G3DSA:2.30.30.40 SH3 Domains 1 64 1.1E-21
11 g13881.t1 Gene3D G3DSA:3.30.1520.10 PX domain 193 324 3.7E-39
13 g13881.t1 Gene3D G3DSA:1.20.1270.60 Arfaptin 367 557 2.3E-64
19 g13881.t1 MobiDBLite mobidb-lite consensus disorder prediction 133 164 -
4 g13881.t1 PANTHER PTHR45827 SORTING NEXIN 2 554 1.7E-149
5 g13881.t1 PRINTS PR00452 SH3 domain signature 1 11 7.0E-7
7 g13881.t1 PRINTS PR00452 SH3 domain signature 15 30 7.0E-7
8 g13881.t1 PRINTS PR00452 SH3 domain signature 33 42 7.0E-7
6 g13881.t1 PRINTS PR00452 SH3 domain signature 45 57 7.0E-7
2 g13881.t1 Pfam PF14604 Variant SH3 domain 5 55 1.7E-11
3 g13881.t1 Pfam PF00787 PX domain 240 316 1.9E-21
1 g13881.t1 Pfam PF10456 WASP-binding domain of Sorting nexin protein 319 557 1.0E-58
20 g13881.t1 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 1 59 28.311
21 g13881.t1 ProSiteProfiles PS50195 PX domain profile. 212 322 17.671
17 g13881.t1 SMART SM00326 SH3_2 1 58 2.9E-20
18 g13881.t1 SMART SM00312 PX_2 209 318 3.6E-18
9 g13881.t1 SUPERFAMILY SSF50044 SH3-domain 2 78 1.97E-21
10 g13881.t1 SUPERFAMILY SSF64268 PX domain 212 319 3.92E-27

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:0005515 protein binding MF
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