General information for g1447.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sorting nexin-32.
Parent gene
- The parent gene g1447 is located on chr_3: 11009768..11010618 (+ 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 | g1447 | g1447.t6 | TSS | g1447.t6 | 11007945 | 11007945 |
| chr_3 | g1447 | g1447.t6 | isoform | g1447.t6 | 11008855 | 11010618 |
| chr_3 | g1447 | g1447.t6 | exon | g1447.t6.exon1 | 11008855 | 11008881 |
| chr_3 | g1447 | g1447.t6 | exon | g1447.t6.exon2 | 11008937 | 11009539 |
| chr_3 | g1447 | g1447.t6 | cds | g1447.t6.CDS1 | 11008946 | 11009539 |
| chr_3 | g1447 | g1447.t6 | exon | g1447.t6.exon3 | 11009760 | 11010618 |
| chr_3 | g1447 | g1447.t6 | cds | g1447.t6.CDS2 | 11009760 | 11009972 |
| chr_3 | g1447 | g1447.t6 | TTS | g1447.t6 | 11010618 | 11010618 |
Sequences
>g1447.t6 Gene=g1447 Length=1489
GCTGAGTATTTAGCGACATTTAAAAAGACTGTCGCAATGCATGAAGTATTTCTTCAAAGA
CTAGCTGCACATTCCGTTTTTCGTAATGATTCACATTTAAAAGTTTTTCTTGAATATGAT
CAAGATTTGTGTGCAAAACCACGCAAAAAGATGGATCTATTTGGAGGTTTAGTTCGTAAT
TTAAGTAAAACAACTGATGAATTGTATTTAGGTGCAACAGTTCGCGATGTAAATGATTTC
TTTGAGAATGAGATGCAATTTTTGACCGAATATCATGCACATTTAAAAGAAGGTGCACAA
CGTAGTGAACGTATGGCAAAGAAACACAAAGAACTCGCTGATAGTTATATAAAAATTTCC
TCATGTCTTGTTCAAATGTCAACAACAGAACAAGGTTCAATGGAGAAATTTACAGCAAAA
ACAGCTGAAATTTTCGAAAAAATGCGCAACATGGAAGGACGTGTAGCAAGCGATCAAGAT
CTTAAGCTAGTTGATACATTGAAATACTATCAAAGAGATAGTAATGCAGCAAAATCTTTA
CTTGTACGTCGATTGCGATGTCTAGCCACTTATGAAGGTGCTAATAGAAATTTAGAAAAG
GCACGCCAAAAGAACAAGGATGTTCATGCTGCTGAAGATTTGCAAACAAAAGCATGCGAG
AAATTTGAAGCAATGTCAGCTCGTGGCAAAGAAGAATTAATGTCATTCCGTAAAAGACGT
GTTGCTGCATTCAAAAAGAGCTTAATTGAGTTAGCGGAACTAGAAGTCAAACATGCTCGA
GCTCAATATGACTTTTTGCGCCAAAGTCTTGAATCAGATCTTCTCAAATTGCAAGATAAC
TAAGTGAATTAAGACAAAAATGCTTCTGTGGTTATCAAAAGACTTTTTCTTCTTTTTCCA
TTTCTGCGATAAGTCGATTGCATAAAATGAATCAACATTTTTTTGTATTGCTATAAATAC
ATCAAATTATTTACTGATAAAGAAATTTTTATTCCATTTCTTTTAAACAAAATGAAGATA
TATATAAAATTATGAAAGAAAATAATTATATTGGCATTCTAATGAACAAAAATTATTTTA
AAAAGTGTAATTTGAATTTAGAAAATTTCGTACTATTGAAAAAGAAGAATTAAGTTTATA
GTTATTATTTGAGTAAAATTAATTGATATCAGCTTCCTTAAAAAATTATTATTTGTTAAT
AATGAATGTCTTTATATCTAAAAAAATATTAACACTCTTCTCTGTATTTATATGTAAAGA
ACTATTTTTTTATTATATGAAAAGTTATAAAGAGCGACCAAATGTCTCTGTTAACCGAAC
TTTAGGAAAATTTAGTTTTTCTGATTTGTACTCCATGAAAATGAGAAGTGACAAAAAGAT
TGATATGACACTAAAATTAAATTTACTATCAAAAGTAAATATAAAGTCAGAAACTTTTTT
TTAGTTCTTCTCTAAATTATATTAAAATATTGAATAAAATGAAAAAAGT
>g1447.t6 Gene=g1447 Length=268
MHEVFLQRLAAHSVFRNDSHLKVFLEYDQDLCAKPRKKMDLFGGLVRNLSKTTDELYLGA
TVRDVNDFFENEMQFLTEYHAHLKEGAQRSERMAKKHKELADSYIKISSCLVQMSTTEQG
SMEKFTAKTAEIFEKMRNMEGRVASDQDLKLVDTLKYYQRDSNAAKSLLVRRLRCLATYE
GANRNLEKARQKNKDVHAAEDLQTKACEKFEAMSARGKEELMSFRKRRVAAFKKSLIELA
ELEVKHARAQYDFLRQSLESDLLKLQDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1447.t6 | CDD | cd07621 | BAR_SNX5_6 | 44 | 260 | 1.23248E-112 |
| 8 | g1447.t6 | Coils | Coil | Coil | 179 | 199 | - |
| 7 | g1447.t6 | Coils | Coil | Coil | 237 | 257 | - |
| 5 | g1447.t6 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 1 | 39 | 9.6E-8 |
| 6 | g1447.t6 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 59 | 260 | 9.6E-39 |
| 2 | g1447.t6 | PANTHER | PTHR45850:SF1 | SORTING NEXIN 6, ISOFORM B | 1 | 259 | 2.4E-105 |
| 3 | g1447.t6 | PANTHER | PTHR45850 | SORTING NEXIN FAMILY MEMBER | 1 | 259 | 2.4E-105 |
| 1 | g1447.t6 | Pfam | PF09325 | Vps5 C terminal like | 59 | 200 | 4.8E-9 |
| 4 | g1447.t6 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 59 | 258 | 2.09E-5 |
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 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.
