General information for g1447.t2
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.t2 | TSS | g1447.t2 | 11007945 | 11007945 |
| chr_3 | g1447 | g1447.t2 | isoform | g1447.t2 | 11008064 | 11009537 |
| chr_3 | g1447 | g1447.t2 | exon | g1447.t2.exon1 | 11008064 | 11008069 |
| chr_3 | g1447 | g1447.t2 | cds | g1447.t2.CDS1 | 11008064 | 11008069 |
| chr_3 | g1447 | g1447.t2 | exon | g1447.t2.exon2 | 11008273 | 11008419 |
| chr_3 | g1447 | g1447.t2 | cds | g1447.t2.CDS2 | 11008273 | 11008419 |
| chr_3 | g1447 | g1447.t2 | exon | g1447.t2.exon3 | 11008474 | 11008509 |
| chr_3 | g1447 | g1447.t2 | cds | g1447.t2.CDS3 | 11008474 | 11008509 |
| chr_3 | g1447 | g1447.t2 | exon | g1447.t2.exon4 | 11008581 | 11008680 |
| chr_3 | g1447 | g1447.t2 | cds | g1447.t2.CDS4 | 11008581 | 11008680 |
| chr_3 | g1447 | g1447.t2 | exon | g1447.t2.exon5 | 11008736 | 11008881 |
| chr_3 | g1447 | g1447.t2 | cds | g1447.t2.CDS5 | 11008736 | 11008881 |
| chr_3 | g1447 | g1447.t2 | exon | g1447.t2.exon6 | 11008937 | 11009537 |
| chr_3 | g1447 | g1447.t2 | cds | g1447.t2.CDS6 | 11008937 | 11009536 |
| chr_3 | g1447 | g1447.t2 | TTS | g1447.t2 | NA | NA |
Sequences
>g1447.t2 Gene=g1447 Length=1036
ATGATGGATGGTGATGATGAAAGTGGAAGTCCACAAAAATCTGTAGCTCCAGAAACTATA
ATAAATAATGAGAACGACCTAAAATCACAAGAAACGTTGCCTGAGAATGCTTTAGTTGTT
GAAATATCTGATGCATTGAGTGAAAAAGATAGAGTAAAATTTACTGTGCATACGAGAACA
ACGATGGCTTGCTTCGCTAAGCAAGACTTTCTCGTTGTTCGACAACATGAAGAATTTGTT
TGGTTGCATGATCGATTTGAAGAGAATGAAGAATATGCCGGATATATAATTCCTCCGGTA
CCACCACGGCCTGATTTCGATGTTTCACGTGAGAAATTACAAAGACTGGGCGAAGGAGAA
GGTTGTATGACTAAAGAAGAATTTAAAAAGATGAAAGCTGAACTAGAGGCTGAGTATTTA
GCGACATTTAAAAAGACTGTCGCAATGCATGAAGTATTTCTTCAAAGACTAGCTGCACAT
TCCGTTTTTCGTAATGATTCACATTTAAAAGTTTTTCTTGAATATGATCAAGATTTGTGT
GCAAAACCACGCAAAAAGATGGATCTATTTGGAGGTTTAGTTCGTAATTTAAGTAAAACA
ACTGATGAATTGTATTTAGGTGCAACAGTTCGCGATGTAAATGATTTCTTTGAGAATGAG
ATGCAATTTTTGACCGAATATCATGCACATTTAAAAGAAGGTGCACAACGTAGTGAACGT
ATGGCAAAGAAACACAAAGAACTCGCTGATAGTTATATAAAAATTTCCTCATGTCTTGTT
CAAATGTCAACAACAGAACAAGGTTCAATGGAGAAATTTACAGCAAAAACAGCTGAAATT
TTCGAAAAAATGCGCAACATGGAAGGACGTGTAGCAAGCGATCAAGATCTTAAGCTAGTT
GATACATTGAAATACTATCAAAGAGATAGTAATGCAGCAAAATCTTTACTTGTACGTCGA
TTGCGATGTCTAGCCACTTATGAAGGTGCTAATAGAAATTTAGAAAAGGCACGCCAAAAG
AACAAGGATGTTCATG
>g1447.t2 Gene=g1447 Length=345
MMDGDDESGSPQKSVAPETIINNENDLKSQETLPENALVVEISDALSEKDRVKFTVHTRT
TMACFAKQDFLVVRQHEEFVWLHDRFEENEEYAGYIIPPVPPRPDFDVSREKLQRLGEGE
GCMTKEEFKKMKAELEAEYLATFKKTVAMHEVFLQRLAAHSVFRNDSHLKVFLEYDQDLC
AKPRKKMDLFGGLVRNLSKTTDELYLGATVRDVNDFFENEMQFLTEYHAHLKEGAQRSER
MAKKHKELADSYIKISSCLVQMSTTEQGSMEKFTAKTAEIFEKMRNMEGRVASDQDLKLV
DTLKYYQRDSNAAKSLLVRRLRCLATYEGANRNLEKARQKNKDVH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1447.t2 | CDD | cd06892 | PX_SNX5_like | 36 | 176 | 3.11335E-83 |
| 8 | g1447.t2 | Coils | Coil | Coil | 327 | 345 | - |
| 6 | g1447.t2 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 29 | 187 | 3.3E-50 |
| 7 | g1447.t2 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 207 | 345 | 2.9E-26 |
| 11 | g1447.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 10 | g1447.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 12 | 28 | - |
| 3 | g1447.t2 | PANTHER | PTHR45850:SF1 | SORTING NEXIN 6, ISOFORM B | 32 | 345 | 1.1E-153 |
| 4 | g1447.t2 | PANTHER | PTHR45850 | SORTING NEXIN FAMILY MEMBER | 32 | 345 | 1.1E-153 |
| 2 | g1447.t2 | Pfam | PF00787 | PX domain | 65 | 176 | 2.8E-15 |
| 1 | g1447.t2 | Pfam | PF09325 | Vps5 C terminal like | 207 | 341 | 3.6E-9 |
| 12 | g1447.t2 | ProSiteProfiles | PS50195 | PX domain profile. | 32 | 179 | 11.383 |
| 5 | g1447.t2 | SUPERFAMILY | SSF64268 | PX domain | 38 | 176 | 2.07E-13 |
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. There were no conditions that were differentially expressed