General information for g1447.t3
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.t3 | TSS | g1447.t3 | 11007945 | 11007945 |
| chr_3 | g1447 | g1447.t3 | isoform | g1447.t3 | 11008064 | 11010618 |
| chr_3 | g1447 | g1447.t3 | exon | g1447.t3.exon1 | 11008064 | 11008069 |
| chr_3 | g1447 | g1447.t3 | exon | g1447.t3.exon2 | 11008273 | 11008453 |
| chr_3 | g1447 | g1447.t3 | exon | g1447.t3.exon3 | 11008581 | 11008680 |
| chr_3 | g1447 | g1447.t3 | exon | g1447.t3.exon4 | 11008736 | 11008881 |
| chr_3 | g1447 | g1447.t3 | cds | g1447.t3.CDS1 | 11008813 | 11008881 |
| chr_3 | g1447 | g1447.t3 | exon | g1447.t3.exon5 | 11008937 | 11009539 |
| chr_3 | g1447 | g1447.t3 | cds | g1447.t3.CDS2 | 11008937 | 11009539 |
| chr_3 | g1447 | g1447.t3 | exon | g1447.t3.exon6 | 11009760 | 11010618 |
| chr_3 | g1447 | g1447.t3 | cds | g1447.t3.CDS3 | 11009760 | 11009972 |
| chr_3 | g1447 | g1447.t3 | TTS | g1447.t3 | 11010618 | 11010618 |
Sequences
>g1447.t3 Gene=g1447 Length=1895
ATGATGGATGGTGATGATGAAAGTGGAAGTCCACAAAAATCTGTAGCTCCAGAAACTATA
ATAAATAATGAGAACGACCTAAAATCACAAGAAACGTTGCCTGAGAATGCTTTAGTTGTT
GAAATATCTGATGCATTGAGTGAAAAAGATAGAGTAAGAACAATTAAAAAATTATAATAC
TCATTAATGCTTCGCTAAGCAAGACTTTCTCGTTGTTCGACAACATGAAGAATTTGTTTG
GTTGCATGATCGATTTGAAGAGAATGAAGAATATGCCGGATATATAATTCCTCCGGTACC
ACCACGGCCTGATTTCGATGTTTCACGTGAGAAATTACAAAGACTGGGCGAAGGAGAAGG
TTGTATGACTAAAGAAGAATTTAAAAAGATGAAAGCTGAACTAGAGGCTGAGTATTTAGC
GACATTTAAAAAGACTGTCGCAATGCATGAAGTATTTCTTCAAAGACTAGCTGCACATTC
CGTTTTTCGTAATGATTCACATTTAAAAGTTTTTCTTGAATATGATCAAGATTTGTGTGC
AAAACCACGCAAAAAGATGGATCTATTTGGAGGTTTAGTTCGTAATTTAAGTAAAACAAC
TGATGAATTGTATTTAGGTGCAACAGTTCGCGATGTAAATGATTTCTTTGAGAATGAGAT
GCAATTTTTGACCGAATATCATGCACATTTAAAAGAAGGTGCACAACGTAGTGAACGTAT
GGCAAAGAAACACAAAGAACTCGCTGATAGTTATATAAAAATTTCCTCATGTCTTGTTCA
AATGTCAACAACAGAACAAGGTTCAATGGAGAAATTTACAGCAAAAACAGCTGAAATTTT
CGAAAAAATGCGCAACATGGAAGGACGTGTAGCAAGCGATCAAGATCTTAAGCTAGTTGA
TACATTGAAATACTATCAAAGAGATAGTAATGCAGCAAAATCTTTACTTGTACGTCGATT
GCGATGTCTAGCCACTTATGAAGGTGCTAATAGAAATTTAGAAAAGGCACGCCAAAAGAA
CAAGGATGTTCATGCTGCTGAAGATTTGCAAACAAAAGCATGCGAGAAATTTGAAGCAAT
GTCAGCTCGTGGCAAAGAAGAATTAATGTCATTCCGTAAAAGACGTGTTGCTGCATTCAA
AAAGAGCTTAATTGAGTTAGCGGAACTAGAAGTCAAACATGCTCGAGCTCAATATGACTT
TTTGCGCCAAAGTCTTGAATCAGATCTTCTCAAATTGCAAGATAACTAAGTGAATTAAGA
CAAAAATGCTTCTGTGGTTATCAAAAGACTTTTTCTTCTTTTTCCATTTCTGCGATAAGT
CGATTGCATAAAATGAATCAACATTTTTTTGTATTGCTATAAATACATCAAATTATTTAC
TGATAAAGAAATTTTTATTCCATTTCTTTTAAACAAAATGAAGATATATATAAAATTATG
AAAGAAAATAATTATATTGGCATTCTAATGAACAAAAATTATTTTAAAAAGTGTAATTTG
AATTTAGAAAATTTCGTACTATTGAAAAAGAAGAATTAAGTTTATAGTTATTATTTGAGT
AAAATTAATTGATATCAGCTTCCTTAAAAAATTATTATTTGTTAATAATGAATGTCTTTA
TATCTAAAAAAATATTAACACTCTTCTCTGTATTTATATGTAAAGAACTATTTTTTTATT
ATATGAAAAGTTATAAAGAGCGACCAAATGTCTCTGTTAACCGAACTTTAGGAAAATTTA
GTTTTTCTGATTTGTACTCCATGAAAATGAGAAGTGACAAAAAGATTGATATGACACTAA
AATTAAATTTACTATCAAAAGTAAATATAAAGTCAGAAACTTTTTTTTAGTTCTTCTCTA
AATTATATTAAAATATTGAATAAAATGAAAAAAGT
>g1447.t3 Gene=g1447 Length=294
MTKEEFKKMKAELEAEYLATFKKTVAMHEVFLQRLAAHSVFRNDSHLKVFLEYDQDLCAK
PRKKMDLFGGLVRNLSKTTDELYLGATVRDVNDFFENEMQFLTEYHAHLKEGAQRSERMA
KKHKELADSYIKISSCLVQMSTTEQGSMEKFTAKTAEIFEKMRNMEGRVASDQDLKLVDT
LKYYQRDSNAAKSLLVRRLRCLATYEGANRNLEKARQKNKDVHAAEDLQTKACEKFEAMS
ARGKEELMSFRKRRVAAFKKSLIELAELEVKHARAQYDFLRQSLESDLLKLQDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1447.t3 | CDD | cd07621 | BAR_SNX5_6 | 70 | 286 | 7.63502E-111 |
| 9 | g1447.t3 | Coils | Coil | Coil | 205 | 225 | - |
| 8 | g1447.t3 | Coils | Coil | Coil | 263 | 283 | - |
| 6 | g1447.t3 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 1 | 65 | 1.6E-17 |
| 7 | g1447.t3 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 85 | 286 | 1.3E-38 |
| 3 | g1447.t3 | PANTHER | PTHR45850:SF1 | SORTING NEXIN 6, ISOFORM B | 1 | 285 | 8.5E-122 |
| 4 | g1447.t3 | PANTHER | PTHR45850 | SORTING NEXIN FAMILY MEMBER | 1 | 285 | 8.5E-122 |
| 2 | g1447.t3 | Pfam | PF00787 | PX domain | 14 | 54 | 1.1E-4 |
| 1 | g1447.t3 | Pfam | PF09325 | Vps5 C terminal like | 85 | 273 | 6.2E-11 |
| 5 | g1447.t3 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 85 | 284 | 2.51E-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. There were no conditions that were differentially expressed