General information for g4403.t1
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.t1 | TSS | g4403.t1 | 1996546 | 1996546 |
| chr_2 | g4403 | g4403.t1 | isoform | g4403.t1 | 1996600 | 1998373 |
| chr_2 | g4403 | g4403.t1 | exon | g4403.t1.exon1 | 1996600 | 1996707 |
| chr_2 | g4403 | g4403.t1 | cds | g4403.t1.CDS1 | 1996600 | 1996707 |
| chr_2 | g4403 | g4403.t1 | exon | g4403.t1.exon2 | 1996929 | 1997095 |
| chr_2 | g4403 | g4403.t1 | cds | g4403.t1.CDS2 | 1996929 | 1997095 |
| chr_2 | g4403 | g4403.t1 | exon | g4403.t1.exon3 | 1997165 | 1997280 |
| chr_2 | g4403 | g4403.t1 | cds | g4403.t1.CDS3 | 1997165 | 1997280 |
| chr_2 | g4403 | g4403.t1 | exon | g4403.t1.exon4 | 1997342 | 1998117 |
| chr_2 | g4403 | g4403.t1 | cds | g4403.t1.CDS4 | 1997342 | 1998117 |
| chr_2 | g4403 | g4403.t1 | exon | g4403.t1.exon5 | 1998170 | 1998373 |
| chr_2 | g4403 | g4403.t1 | cds | g4403.t1.CDS5 | 1998170 | 1998373 |
| chr_2 | g4403 | g4403.t1 | TTS | g4403.t1 | 1998976 | 1998976 |
Sequences
>g4403.t1 Gene=g4403 Length=1371
ATGGAAAATTCTTCTTTGCCGCCTCTTTTTGACGACAATATGCAAAATGTGGATATCAGT
TCACCCAATGAAGTTGAGCAATCATTATTTGAGTCAGCGATGGAAGAGGAAAATGATCTC
ATTCAAACACCAACTTTGAAAGAGAGTAATGCAGCAATTATGGAAGATGTGATAACAACA
TCTGATGAAAGAGAAACCAATGGACATTATATTGAAATTTCTGTTGAGGAGCCACAAAAA
ATGGGAGATGGCATGAATAGTTATTTAGTTTACAAAGTTATAACAAAAACTAATATACCC
AAGTTTTCGCGAAGACAATCAACTGTACTTCGAAGATTCAGTGACTTTTTGGGACTTCAT
GAACAACTTGTTGAACGTTATTTACGAGCTGGTTTTATTATTCCTCCTGCTCCATCGAAG
AATATTTTAGGTGCTACAAAAGTTAAAATGGGAACTCAACAGAATATTGAACCAGGCGCT
GCCACAAATGCGCAAGAATGGGTAGAAAATCGTCGTGCGAGTTTGGAGAGATTTTTGAAT
AGAACTGCAGCTCATCCAACGCTTCGACATGATAGCAATTTCATTCATTTTCTTGAAAAT
GAACAAGATTTACCTCGTGCAACAAACACTGCTGCTCTAAGTGGTGCTGGCGTTATGAGG
CTATTTAACAAAGTTGGTGAAACTGTGAACAAAATTACATACAAAATGGATGAAAATGAT
ACATGGTTTGCTGATAAAATACAAGAGATTGATTCTCTTGATTCTCATTACCAAAAGTTG
CATATTGCTGTAAAATCGCTAGTTGCACATCGACAAGAATTAGCACACTTAACAGGAAAT
GTTGCTAAATCTGCAGCTATGCTGAGTACATGTGAGGAACATGTTGGTCTTTCAAAAGCC
TTATCACAACTAGCAGATGTTGAGGAAAAAATTGAAATATTAAGGTCTGAACAGTCAAAT
TCAGATTTTTATATTCTATCAGAGATGATTAAAGATTACATTGGCTTGCTTGGTGCTATC
AAAGATGTTTTTCATGAACGTGTTAAAGTTTTTCAAAATTGGCAACATGCTCAGACTCAG
TTAACAAAGAAACGAGAGAATAAAGCAAAATTGGAATTGAATCAACGCAATGATAAAATT
GATCAAGCTCAGAAAGAAGTTGAAGAGTGGGAAACAAAAGTGCAACGTTGTCAGAAAGAA
TTTGAAGACATTTCTGCAGAAATAAAACGTGAAGTTGAACGCTTTGAAATAAATAGAGCA
AAGGACTTTAAGTCGACTATTATCAAATATTTACAAGATCAGATGGCTCATCAGCAGCAA
ATTATGAAATATTGGGAAAATTATATGCCTGCGGCAAAAGAAATTGCATGA
>g4403.t1 Gene=g4403 Length=456
MENSSLPPLFDDNMQNVDISSPNEVEQSLFESAMEEENDLIQTPTLKESNAAIMEDVITT
SDERETNGHYIEISVEEPQKMGDGMNSYLVYKVITKTNIPKFSRRQSTVLRRFSDFLGLH
EQLVERYLRAGFIIPPAPSKNILGATKVKMGTQQNIEPGAATNAQEWVENRRASLERFLN
RTAAHPTLRHDSNFIHFLENEQDLPRATNTAALSGAGVMRLFNKVGETVNKITYKMDEND
TWFADKIQEIDSLDSHYQKLHIAVKSLVAHRQELAHLTGNVAKSAAMLSTCEEHVGLSKA
LSQLADVEEKIEILRSEQSNSDFYILSEMIKDYIGLLGAIKDVFHERVKVFQNWQHAQTQ
LTKKRENKAKLELNQRNDKIDQAQKEVEEWETKVQRCQKEFEDISAEIKREVERFEINRA
KDFKSTIIKYLQDQMAHQQQIMKYWENYMPAAKEIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4403.t1 | CDD | cd06859 | PX_SNX1_2_like | 71 | 201 | 1.01904E-56 |
| 12 | g4403.t1 | CDD | cd07623 | BAR_SNX1_2 | 230 | 453 | 1.94316E-124 |
| 10 | g4403.t1 | Coils | Coil | Coil | 297 | 317 | - |
| 9 | g4403.t1 | Coils | Coil | Coil | 366 | 414 | - |
| 7 | g4403.t1 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 62 | 211 | 8.8E-41 |
| 8 | g4403.t1 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 234 | 456 | 8.8E-70 |
| 3 | g4403.t1 | PANTHER | PTHR10555 | SORTING NEXIN | 24 | 456 | 3.6E-138 |
| 4 | g4403.t1 | PANTHER | PTHR10555:SF129 | SORTING NEXIN-1 | 24 | 456 | 3.6E-138 |
| 2 | g4403.t1 | Pfam | PF00787 | PX domain | 101 | 200 | 1.3E-19 |
| 1 | g4403.t1 | Pfam | PF09325 | Vps5 C terminal like | 219 | 450 | 1.6E-84 |
| 14 | g4403.t1 | ProSiteProfiles | PS50195 | PX domain profile. | 69 | 205 | 18.636 |
| 13 | g4403.t1 | SMART | SM00312 | PX_2 | 68 | 201 | 2.3E-26 |
| 6 | g4403.t1 | SUPERFAMILY | SSF64268 | PX domain | 66 | 201 | 1.06E-28 |
| 5 | g4403.t1 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 240 | 450 | 6.54E-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 transcript has been annotated with K17917 (sorting nexin-1/2)
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.
