General information for g4403.t3
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.t3 | TSS | g4403.t3 | 1996546 | 1996546 |
| chr_2 | g4403 | g4403.t3 | isoform | g4403.t3 | 1996600 | 1998097 |
| chr_2 | g4403 | g4403.t3 | exon | g4403.t3.exon1 | 1996600 | 1997095 |
| chr_2 | g4403 | g4403.t3 | cds | g4403.t3.CDS1 | 1996980 | 1997095 |
| chr_2 | g4403 | g4403.t3 | exon | g4403.t3.exon2 | 1997165 | 1997280 |
| chr_2 | g4403 | g4403.t3 | cds | g4403.t3.CDS2 | 1997165 | 1997280 |
| chr_2 | g4403 | g4403.t3 | exon | g4403.t3.exon3 | 1997342 | 1998097 |
| chr_2 | g4403 | g4403.t3 | cds | g4403.t3.CDS3 | 1997342 | 1998096 |
| chr_2 | g4403 | g4403.t3 | TTS | g4403.t3 | 1998976 | 1998976 |
Sequences
>g4403.t3 Gene=g4403 Length=1368
ATGGAAAATTCTTCTTTGCCGCCTCTTTTTGACGACAATATGCAAAATGTGGATATCAGT
TCACCCAATGAAGTTGAGCAATCATTATTTGAGTCAGCGATGGAAGAGGTAATTCAAATT
TTTTAAAAAAATTGCGATGAGAAAAATTATTAATCATCATTTTCTCATTTGTTAAATTTC
TTATCGCAAAACAGTTATTATTTTATATATGACGCTTTATCGGTTTCGAGCTGCACTTTT
ACAATTAATGATTTGTTTCTATAATTCGCCTTTATTGAATCAACAAAAATATGCGGGTGA
TGAATGTAATACATTTTTTTTTGATTTAGGAAAATGATCTCATTCAAACACCAACTTTGA
AAGAGAGTAATGCAGCAATTATGGAAGATGTGATAACAACATCTGATGAAAGAGAAACCA
ATGGACATTATATTGAAATTTCTGTTGAGGAGCCACAAAAAATGGGAGATGGCATGAATA
GTTATTTAGTTTACAAAGTTATAACAAAAACTAATATACCCAAGTTTTCGCGAAGACAAT
CAACTGTACTTCGAAGATTCAGTGACTTTTTGGGACTTCATGAACAACTTGTTGAACGTT
ATTTACGAGCTGGTTTTATTATTCCTCCTGCTCCATCGAAGAATATTTTAGGTGCTACAA
AAGTTAAAATGGGAACTCAACAGAATATTGAACCAGGCGCTGCCACAAATGCGCAAGAAT
GGGTAGAAAATCGTCGTGCGAGTTTGGAGAGATTTTTGAATAGAACTGCAGCTCATCCAA
CGCTTCGACATGATAGCAATTTCATTCATTTTCTTGAAAATGAACAAGATTTACCTCGTG
CAACAAACACTGCTGCTCTAAGTGGTGCTGGCGTTATGAGGCTATTTAACAAAGTTGGTG
AAACTGTGAACAAAATTACATACAAAATGGATGAAAATGATACATGGTTTGCTGATAAAA
TACAAGAGATTGATTCTCTTGATTCTCATTACCAAAAGTTGCATATTGCTGTAAAATCGC
TAGTTGCACATCGACAAGAATTAGCACACTTAACAGGAAATGTTGCTAAATCTGCAGCTA
TGCTGAGTACATGTGAGGAACATGTTGGTCTTTCAAAAGCCTTATCACAACTAGCAGATG
TTGAGGAAAAAATTGAAATATTAAGGTCTGAACAGTCAAATTCAGATTTTTATATTCTAT
CAGAGATGATTAAAGATTACATTGGCTTGCTTGGTGCTATCAAAGATGTTTTTCATGAAC
GTGTTAAAGTTTTTCAAAATTGGCAACATGCTCAGACTCAGTTAACAAAGAAACGAGAGA
ATAAAGCAAAATTGGAATTGAATCAACGCAATGATAAAATTGATCAAG
>g4403.t3 Gene=g4403 Length=329
MEDVITTSDERETNGHYIEISVEEPQKMGDGMNSYLVYKVITKTNIPKFSRRQSTVLRRF
SDFLGLHEQLVERYLRAGFIIPPAPSKNILGATKVKMGTQQNIEPGAATNAQEWVENRRA
SLERFLNRTAAHPTLRHDSNFIHFLENEQDLPRATNTAALSGAGVMRLFNKVGETVNKIT
YKMDENDTWFADKIQEIDSLDSHYQKLHIAVKSLVAHRQELAHLTGNVAKSAAMLSTCEE
HVGLSKALSQLADVEEKIEILRSEQSNSDFYILSEMIKDYIGLLGAIKDVFHERVKVFQN
WQHAQTQLTKKRENKAKLELNQRNDKIDQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4403.t3 | CDD | cd06859 | PX_SNX1_2_like | 18 | 148 | 3.27605E-58 |
| 8 | g4403.t3 | Coils | Coil | Coil | 244 | 264 | - |
| 9 | g4403.t3 | Coils | Coil | Coil | 310 | 329 | - |
| 6 | g4403.t3 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 9 | 158 | 4.4E-41 |
| 7 | g4403.t3 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 181 | 329 | 3.4E-42 |
| 3 | g4403.t3 | PANTHER | PTHR10555 | SORTING NEXIN | 9 | 329 | 3.6E-110 |
| 4 | g4403.t3 | PANTHER | PTHR10555:SF129 | SORTING NEXIN-1 | 9 | 329 | 3.6E-110 |
| 2 | g4403.t3 | Pfam | PF00787 | PX domain | 48 | 147 | 6.9E-20 |
| 1 | g4403.t3 | Pfam | PF09325 | Vps5 C terminal like | 166 | 329 | 3.1E-56 |
| 12 | g4403.t3 | ProSiteProfiles | PS50195 | PX domain profile. | 16 | 152 | 18.636 |
| 11 | g4403.t3 | SMART | SM00312 | PX_2 | 15 | 148 | 2.3E-26 |
| 5 | g4403.t3 | SUPERFAMILY | SSF64268 | PX domain | 13 | 148 | 5.36E-29 |
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. There were no conditions that were differentially expressed