General information for g4403.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sorting nexin-2.
Parent gene
- The parent gene g4403 is located on chr_2: 1998168..1998984 (+ 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_2 | g4403 | g4403.t8 | TSS | g4403.t8 | 1996936 | 1996936 |
| chr_2 | g4403 | g4403.t8 | isoform | g4403.t8 | 1997188 | 1998984 |
| chr_2 | g4403 | g4403.t8 | exon | g4403.t8.exon1 | 1997188 | 1997288 |
| chr_2 | g4403 | g4403.t8 | cds | g4403.t8.CDS1 | 1997248 | 1997288 |
| chr_2 | g4403 | g4403.t8 | exon | g4403.t8.exon2 | 1997355 | 1998117 |
| chr_2 | g4403 | g4403.t8 | cds | g4403.t8.CDS2 | 1997355 | 1998117 |
| chr_2 | g4403 | g4403.t8 | exon | g4403.t8.exon3 | 1998170 | 1998984 |
| chr_2 | g4403 | g4403.t8 | cds | g4403.t8.CDS3 | 1998170 | 1998373 |
| chr_2 | g4403 | g4403.t8 | TTS | g4403.t8 | 1998976 | 1998976 |
Sequences
>g4403.t8 Gene=g4403 Length=1679
CCAAGTTTTCGCGAAGACAATCAACTGTACTTCGAAGATTCAGTGACTTTTTGGGACTTC
ATGAACAACTTGTTGAACGTTATTTACGAGCTGGTTAGACATCCTGCTCCATCGAAGAAT
ATTTTAGGTGCTACAAAAGTTAAAATGGGAACTCAACAGAATATTGAACCAGGCGCTGCC
ACAAATGCGCAAGAATGGGTAGAAAATCGTCGTGCGAGTTTGGAGAGATTTTTGAATAGA
ACTGCAGCTCATCCAACGCTTCGACATGATAGCAATTTCATTCATTTTCTTGAAAATGAA
CAAGATTTACCTCGTGCAACAAACACTGCTGCTCTAAGTGGTGCTGGCGTTATGAGGCTA
TTTAACAAAGTTGGTGAAACTGTGAACAAAATTACATACAAAATGGATGAAAATGATACA
TGGTTTGCTGATAAAATACAAGAGATTGATTCTCTTGATTCTCATTACCAAAAGTTGCAT
ATTGCTGTAAAATCGCTAGTTGCACATCGACAAGAATTAGCACACTTAACAGGAAATGTT
GCTAAATCTGCAGCTATGCTGAGTACATGTGAGGAACATGTTGGTCTTTCAAAAGCCTTA
TCACAACTAGCAGATGTTGAGGAAAAAATTGAAATATTAAGGTCTGAACAGTCAAATTCA
GATTTTTATATTCTATCAGAGATGATTAAAGATTACATTGGCTTGCTTGGTGCTATCAAA
GATGTTTTTCATGAACGTGTTAAAGTTTTTCAAAATTGGCAACATGCTCAGACTCAGTTA
ACAAAGAAACGAGAGAATAAAGCAAAATTGGAATTGAATCAACGCAATGATAAAATTGAT
CAAGCTCAGAAAGAAGTTGAAGAGTGGGAAACAAAAGTGCAACGTTGTCAGAAAGAATTT
GAAGACATTTCTGCAGAAATAAAACGTGAAGTTGAACGCTTTGAAATAAATAGAGCAAAG
GACTTTAAGTCGACTATTATCAAATATTTACAAGATCAGATGGCTCATCAGCAGCAAATT
ATGAAATATTGGGAAAATTATATGCCTGCGGCAAAAGAAATTGCATGAAACACAGCAACT
GTTTTAAAGAAATCTGATAAGGTTCATCTTATTGTGTGAGCTTTTTTTGCTTTTATAACA
GCAGGTTAAAATATTTTTTCGTACTATCTACACATTTTTTTGACAATTTTCCTTCTCTCA
GTTTTTCATGCTGCTGAAAAACAAAATATCATGTATGTCCTATATTTGTTTACGTCAACC
TCAATGATCTTTTCTTAAAAAGATTATATTTTATGAAATTAGTTTAATCGATCAACTATT
GATTCGCTATTGCTTTTCATTCATTATTTTTTGATACGTATGTGTATATCACCCAAAAAA
ACACACGTAACATTGTATAATTTATACATAAAACTTTTTTATACATCAATAATGTTTAAA
CATTCCGAAGAAATATTTGTTAAAATAATGATAACGTCATTATAACTTTATATATTGTAT
GAATGTATTCATATTATGATTTTACATAAATCAATTTCATATTGATATATTTTGAAGATG
AGAGAAAAAATAAGAAATCATTTTGAATATTATAAAAAAAGGTTTATTCTTTATATTATT
AGAGGATAATGTTTATAAATCACGAATAAATTATTTAATCACTTTATTCGAATATGCTC
>g4403.t8 Gene=g4403 Length=335
MNNLLNVIYELVRHPAPSKNILGATKVKMGTQQNIEPGAATNAQEWVENRRASLERFLNR
TAAHPTLRHDSNFIHFLENEQDLPRATNTAALSGAGVMRLFNKVGETVNKITYKMDENDT
WFADKIQEIDSLDSHYQKLHIAVKSLVAHRQELAHLTGNVAKSAAMLSTCEEHVGLSKAL
SQLADVEEKIEILRSEQSNSDFYILSEMIKDYIGLLGAIKDVFHERVKVFQNWQHAQTQL
TKKRENKAKLELNQRNDKIDQAQKEVEEWETKVQRCQKEFEDISAEIKREVERFEINRAK
DFKSTIIKYLQDQMAHQQQIMKYWENYMPAAKEIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4403.t8 | CDD | cd07623 | BAR_SNX1_2 | 109 | 332 | 7.92022E-124 |
| 9 | g4403.t8 | Coils | Coil | Coil | 176 | 196 | - |
| 10 | g4403.t8 | Coils | Coil | Coil | 245 | 293 | - |
| 7 | g4403.t8 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 2 | 90 | 1.1E-15 |
| 8 | g4403.t8 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 113 | 335 | 3.8E-70 |
| 3 | g4403.t8 | PANTHER | PTHR10555 | SORTING NEXIN | 12 | 335 | 2.5E-107 |
| 4 | g4403.t8 | PANTHER | PTHR10555:SF129 | SORTING NEXIN-1 | 12 | 335 | 2.5E-107 |
| 2 | g4403.t8 | Pfam | PF00787 | PX domain | 11 | 79 | 1.8E-8 |
| 1 | g4403.t8 | Pfam | PF09325 | Vps5 C terminal like | 98 | 329 | 6.9E-85 |
| 11 | g4403.t8 | ProSiteProfiles | PS50195 | PX domain profile. | 1 | 84 | 9.92 |
| 6 | g4403.t8 | SUPERFAMILY | SSF64268 | PX domain | 3 | 80 | 1.01E-8 |
| 5 | g4403.t8 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 119 | 329 | 2.43E-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
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.
