General information for g15754.t1
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.t1 | TTS | g15754.t1 | 6669009 | 6669009 |
| chr_4 | g15754 | g15754.t1 | isoform | g15754.t1 | 6669147 | 6669713 |
| chr_4 | g15754 | g15754.t1 | exon | g15754.t1.exon1 | 6669147 | 6669473 |
| chr_4 | g15754 | g15754.t1 | cds | g15754.t1.CDS1 | 6669147 | 6669473 |
| chr_4 | g15754 | g15754.t1 | exon | g15754.t1.exon2 | 6669534 | 6669713 |
| chr_4 | g15754 | g15754.t1 | cds | g15754.t1.CDS2 | 6669534 | 6669713 |
| chr_4 | g15754 | g15754.t1 | TSS | g15754.t1 | 6669650 | 6669650 |
Sequences
>g15754.t1 Gene=g15754 Length=507
ATGAATTCACCCGAAGAAAATTTCGAGAACAATTCAATATCTCGATTAGCCACAAAAAAG
CAAAGTTTAGATGACATGTATTCAGTGCCAGCTAATTTCTTAGAAATTGATGTTGTCAAT
CCACAGACAAAAATTATAGCTGGAAAAAAGAAGTATACAGATTATGAGATTCGTATGAAG
ACTAATCTTCCAGTTTTCAAAATAAAAGAATCCAGCGTTCGTCGTCGTTATTCAGACTTT
GAATGGCTTCGTAATGAACTTGAACGTGACAGTAAAATTGTTGTGCCACCTTTACCATCA
AAAGCATGGAAAAGGCAACTTCCATTTTGGAGTGATGATGGATTATTTGATGAGAATTTT
ATTGAAGAAAGAAGAAAAGGACTAGAAATTTTTGTTAACAAAATCGCAGGGCATCCGCTT
GCACAGAATGAGAGATGTTTGCATATGTTCTTACAAGAACCTGTTATTGATCGAGGTTAC
ACACCTGGTAAAGTAAGAAATGCTTAA
>g15754.t1 Gene=g15754 Length=168
MNSPEENFENNSISRLATKKQSLDDMYSVPANFLEIDVVNPQTKIIAGKKKYTDYEIRMK
TNLPVFKIKESSVRRRYSDFEWLRNELERDSKIVVPPLPSKAWKRQLPFWSDDGLFDENF
IEERRKGLEIFVNKIAGHPLAQNERCLHMFLQEPVIDRGYTPGKVRNA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g15754.t1 | CDD | cd06894 | PX_SNX3_like | 33 | 156 | 0.000 |
| 6 | g15754.t1 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 27 | 165 | 0.000 |
| 2 | g15754.t1 | PANTHER | PTHR45963:SF3 | SORTING NEXIN-12 | 14 | 167 | 0.000 |
| 3 | g15754.t1 | PANTHER | PTHR45963 | RE52028P | 14 | 167 | 0.000 |
| 1 | g15754.t1 | Pfam | PF00787 | PX domain | 65 | 153 | 0.000 |
| 7 | g15754.t1 | ProSiteProfiles | PS50195 | PX domain profile. | 33 | 157 | 17.978 |
| 5 | g15754.t1 | SMART | SM00312 | PX_2 | 31 | 154 | 0.000 |
| 4 | g15754.t1 | SUPERFAMILY | SSF64268 | PX domain | 31 | 154 | 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 transcript has been annotated with K17918 (sorting nexin-3/12)
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.
