General information for g3842.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sorting nexin-12.
Parent gene
- The parent gene g3842 is located on chr_3: 28332517..28333098 (+ 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_3 | g3842 | g3842.t1 | isoform | g3842.t1 | 28331714 | 28332937 |
| chr_3 | g3842 | g3842.t1 | exon | g3842.t1.exon1 | 28331714 | 28331779 |
| chr_3 | g3842 | g3842.t1 | cds | g3842.t1.CDS1 | 28331714 | 28331779 |
| chr_3 | g3842 | g3842.t1 | exon | g3842.t1.exon2 | 28331859 | 28331867 |
| chr_3 | g3842 | g3842.t1 | cds | g3842.t1.CDS2 | 28331859 | 28331867 |
| chr_3 | g3842 | g3842.t1 | exon | g3842.t1.exon3 | 28331943 | 28332116 |
| chr_3 | g3842 | g3842.t1 | cds | g3842.t1.CDS3 | 28331943 | 28332116 |
| chr_3 | g3842 | g3842.t1 | exon | g3842.t1.exon4 | 28332499 | 28332808 |
| chr_3 | g3842 | g3842.t1 | cds | g3842.t1.CDS4 | 28332499 | 28332808 |
| chr_3 | g3842 | g3842.t1 | exon | g3842.t1.exon5 | 28332879 | 28332937 |
| chr_3 | g3842 | g3842.t1 | cds | g3842.t1.CDS5 | 28332879 | 28332937 |
| chr_3 | g3842 | g3842.t1 | TTS | g3842.t1 | 28333111 | 28333111 |
| chr_3 | g3842 | g3842.t1 | TSS | g3842.t1 | NA | NA |
Sequences
>g3842.t1 Gene=g3842 Length=618
ATGCGAAAAATTTATCATTTTCGAAGAAATTTAGTGCTCGAAACAACCACAACGTGCGCT
GAAGTTATATTATTAAAAATGAATGATGATTTTGAAAATAGTTCGATCTCTCGATTGCAC
ACAAAAAAGCAATCTCTGGATGATATGTATTCTGCTCCAGCTAATTTTCTTGAAATAGAT
GTACTAAATCCACAAACAACAATTGTCCAGGGGAAGAAAAAGTTTACAGATTATGAAATA
AGAATGAAGACAAATCTGCCAGTGTTCAAGGTAAAAGAGTCAAGTGTACGACGCAGATAT
TCAGATTTTGAATGGTTAAGGAATGAACTTGAGCGCGATTCAAAAATTATAGTTCCGCCA
CTTCCTTCAAAAGCATGGAAGAGACAAGTACCTTTTTTCGGTGGCGATGAAGGAATATTT
GAGGAGAAATTCATTGAAGAAAGACGTAAAGGATTGGAAATATTTGTTAATAAAATAGCA
GGGCATCCATTGGCTCAAAACGAGAAATGTTTACATATGTTTTTACAGGAAGAGACCATT
GATCGAAATTATACACCCGGAAAAGACTATTTCAAATTATATGTTATTGCACTCATATTA
TTTTATATATCAGTATAA
>g3842.t1 Gene=g3842 Length=205
MRKIYHFRRNLVLETTTTCAEVILLKMNDDFENSSISRLHTKKQSLDDMYSAPANFLEID
VLNPQTTIVQGKKKFTDYEIRMKTNLPVFKVKESSVRRRYSDFEWLRNELERDSKIIVPP
LPSKAWKRQVPFFGGDEGIFEEKFIEERRKGLEIFVNKIAGHPLAQNEKCLHMFLQEETI
DRNYTPGKDYFKLYVIALILFYISV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g3842.t1 | CDD | cd06894 | PX_SNX3_like | 56 | 180 | 0.000 |
| 6 | g3842.t1 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 50 | 191 | 0.000 |
| 2 | g3842.t1 | PANTHER | PTHR45963:SF3 | SORTING NEXIN-12 | 36 | 191 | 0.000 |
| 3 | g3842.t1 | PANTHER | PTHR45963 | RE52028P | 36 | 191 | 0.000 |
| 1 | g3842.t1 | Pfam | PF00787 | PX domain | 88 | 177 | 0.000 |
| 7 | g3842.t1 | ProSiteProfiles | PS50195 | PX domain profile. | 56 | 181 | 18.109 |
| 5 | g3842.t1 | SMART | SM00312 | PX_2 | 54 | 178 | 0.000 |
| 4 | g3842.t1 | SUPERFAMILY | SSF64268 | PX domain | 53 | 178 | 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.
