General information for g15754.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sorting nexin-3.
Parent gene
- The parent gene g15754 is located on chr_4: 6669147..6669713 (- strand)
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.t7 | TTS | g15754.t7 | 6667930 | 6667930 |
| chr_4 | g15754 | g15754.t7 | isoform | g15754.t7 | 6668743 | 6669713 |
| chr_4 | g15754 | g15754.t7 | exon | g15754.t7.exon1 | 6668743 | 6669084 |
| chr_4 | g15754 | g15754.t7 | cds | g15754.t7.CDS1 | 6669047 | 6669084 |
| chr_4 | g15754 | g15754.t7 | exon | g15754.t7.exon2 | 6669167 | 6669713 |
| chr_4 | g15754 | g15754.t7 | cds | g15754.t7.CDS2 | 6669167 | 6669713 |
| chr_4 | g15754 | g15754.t7 | TSS | g15754.t7 | 6669650 | 6669650 |
Sequences
>g15754.t7 Gene=g15754 Length=889
ATGAATTCACCCGAAGAAAATTTCGAGAACAATTCAATATCTCGATTAGCCACAAAAAAG
CAAAGTTTAGATGACATGTATTCAGTGCCAGCTAATTTCTTAGAAATTGATGTTGTCAAT
CCACAGACAAAAATTATAGCTGGAAAAAAGAAGTATACAGATTATGAGATTCGTATGAAG
GTAAGAAAAATTAGAATTTTTTTATCATCAATGACTCATCAATGTTTTCTTTTTTTAAAG
ACTAATCTTCCAGTTTTCAAAATAAAAGAATCCAGCGTTCGTCGTCGTTATTCAGACTTT
GAATGGCTTCGTAATGAACTTGAACGTGACAGTAAAATTGTTGTGCCACCTTTACCATCA
AAAGCATGGAAAAGGCAACTTCCATTTTGGAGTGATGATGGATTATTTGATGAGAATTTT
ATTGAAGAAAGAAGAAAAGGACTAGAAATTTTTGTTAACAAAATCGCAGGGCATCCGCTT
GCACAGAATGAGAGATGTTTGCATATGTTCTTACAAGAACCTGTTATTGATCGAGGTTAC
ACACCTGAAATTGTAGATTTAGCCAATGTCTACAGATTTTCTTAAACTTAATGTGAGATT
ATATATGAGCATTTTTATCAAATAATTTAACTTTCATTCAAATTTCATTTATTATTTTTA
GACATGGTTTGATATGTCTTGACAAAAAGTTGTACTATTTTTTAATTAAATTTATTTTAT
TCCGTACAATAATTTAAATTACAGACAGCTGATTATAATAATTTTCATTTCATCACTATT
GACTTTTTAGAATTTAAAAGTTTTCTCAGCTCAAAAATATTTTAAACACTTCCATAAAAA
TTAAATTATAAAATAAAAATATCCTTTCACTAAAACCTTAAAAAGCCAA
>g15754.t7 Gene=g15754 Length=194
MNSPEENFENNSISRLATKKQSLDDMYSVPANFLEIDVVNPQTKIIAGKKKYTDYEIRMK
VRKIRIFLSSMTHQCFLFLKTNLPVFKIKESSVRRRYSDFEWLRNELERDSKIVVPPLPS
KAWKRQLPFWSDDGLFDENFIEERRKGLEIFVNKIAGHPLAQNERCLHMFLQEPVIDRGY
TPEIVDLANVYRFS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g15754.t7 | CDD | cd06894 | PX_SNX3_like | 33 | 176 | 0.000 |
| 8 | g15754.t7 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 27 | 183 | 0.000 |
| 3 | g15754.t7 | PANTHER | PTHR45963:SF3 | SORTING NEXIN-12 | 14 | 62 | 0.000 |
| 5 | g15754.t7 | PANTHER | PTHR45963 | RE52028P | 14 | 62 | 0.000 |
| 2 | g15754.t7 | PANTHER | PTHR45963:SF3 | SORTING NEXIN-12 | 79 | 185 | 0.000 |
| 4 | g15754.t7 | PANTHER | PTHR45963 | RE52028P | 79 | 185 | 0.000 |
| 1 | g15754.t7 | Pfam | PF00787 | PX domain | 86 | 173 | 0.000 |
| 9 | g15754.t7 | ProSiteProfiles | PS50195 | PX domain profile. | 33 | 177 | 17.115 |
| 7 | g15754.t7 | SMART | SM00312 | PX_2 | 31 | 174 | 0.000 |
| 6 | g15754.t7 | SUPERFAMILY | SSF64268 | PX domain | 32 | 174 | 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
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.
