General information for g1447.t1
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.t1 | TSS | g1447.t1 | 11007945 | 11007945 |
| chr_3 | g1447 | g1447.t1 | isoform | g1447.t1 | 11008064 | 11009972 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon1 | 11008064 | 11008069 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS1 | 11008064 | 11008069 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon2 | 11008273 | 11008419 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS2 | 11008273 | 11008419 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon3 | 11008474 | 11008509 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS3 | 11008474 | 11008509 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon4 | 11008581 | 11008680 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS4 | 11008581 | 11008680 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon5 | 11008736 | 11008881 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS5 | 11008736 | 11008881 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon6 | 11008937 | 11009539 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS6 | 11008937 | 11009539 |
| chr_3 | g1447 | g1447.t1 | exon | g1447.t1.exon7 | 11009760 | 11009972 |
| chr_3 | g1447 | g1447.t1 | cds | g1447.t1.CDS7 | 11009760 | 11009972 |
| chr_3 | g1447 | g1447.t1 | TTS | g1447.t1 | 11010618 | 11010618 |
Sequences
>g1447.t1 Gene=g1447 Length=1251
ATGATGGATGGTGATGATGAAAGTGGAAGTCCACAAAAATCTGTAGCTCCAGAAACTATA
ATAAATAATGAGAACGACCTAAAATCACAAGAAACGTTGCCTGAGAATGCTTTAGTTGTT
GAAATATCTGATGCATTGAGTGAAAAAGATAGAGTAAAATTTACTGTGCATACGAGAACA
ACGATGGCTTGCTTCGCTAAGCAAGACTTTCTCGTTGTTCGACAACATGAAGAATTTGTT
TGGTTGCATGATCGATTTGAAGAGAATGAAGAATATGCCGGATATATAATTCCTCCGGTA
CCACCACGGCCTGATTTCGATGTTTCACGTGAGAAATTACAAAGACTGGGCGAAGGAGAA
GGTTGTATGACTAAAGAAGAATTTAAAAAGATGAAAGCTGAACTAGAGGCTGAGTATTTA
GCGACATTTAAAAAGACTGTCGCAATGCATGAAGTATTTCTTCAAAGACTAGCTGCACAT
TCCGTTTTTCGTAATGATTCACATTTAAAAGTTTTTCTTGAATATGATCAAGATTTGTGT
GCAAAACCACGCAAAAAGATGGATCTATTTGGAGGTTTAGTTCGTAATTTAAGTAAAACA
ACTGATGAATTGTATTTAGGTGCAACAGTTCGCGATGTAAATGATTTCTTTGAGAATGAG
ATGCAATTTTTGACCGAATATCATGCACATTTAAAAGAAGGTGCACAACGTAGTGAACGT
ATGGCAAAGAAACACAAAGAACTCGCTGATAGTTATATAAAAATTTCCTCATGTCTTGTT
CAAATGTCAACAACAGAACAAGGTTCAATGGAGAAATTTACAGCAAAAACAGCTGAAATT
TTCGAAAAAATGCGCAACATGGAAGGACGTGTAGCAAGCGATCAAGATCTTAAGCTAGTT
GATACATTGAAATACTATCAAAGAGATAGTAATGCAGCAAAATCTTTACTTGTACGTCGA
TTGCGATGTCTAGCCACTTATGAAGGTGCTAATAGAAATTTAGAAAAGGCACGCCAAAAG
AACAAGGATGTTCATGCTGCTGAAGATTTGCAAACAAAAGCATGCGAGAAATTTGAAGCA
ATGTCAGCTCGTGGCAAAGAAGAATTAATGTCATTCCGTAAAAGACGTGTTGCTGCATTC
AAAAAGAGCTTAATTGAGTTAGCGGAACTAGAAGTCAAACATGCTCGAGCTCAATATGAC
TTTTTGCGCCAAAGTCTTGAATCAGATCTTCTCAAATTGCAAGATAACTAA
>g1447.t1 Gene=g1447 Length=416
MMDGDDESGSPQKSVAPETIINNENDLKSQETLPENALVVEISDALSEKDRVKFTVHTRT
TMACFAKQDFLVVRQHEEFVWLHDRFEENEEYAGYIIPPVPPRPDFDVSREKLQRLGEGE
GCMTKEEFKKMKAELEAEYLATFKKTVAMHEVFLQRLAAHSVFRNDSHLKVFLEYDQDLC
AKPRKKMDLFGGLVRNLSKTTDELYLGATVRDVNDFFENEMQFLTEYHAHLKEGAQRSER
MAKKHKELADSYIKISSCLVQMSTTEQGSMEKFTAKTAEIFEKMRNMEGRVASDQDLKLV
DTLKYYQRDSNAAKSLLVRRLRCLATYEGANRNLEKARQKNKDVHAAEDLQTKACEKFEA
MSARGKEELMSFRKRRVAAFKKSLIELAELEVKHARAQYDFLRQSLESDLLKLQDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g1447.t1 | CDD | cd06892 | PX_SNX5_like | 36 | 176 | 1.06153E-81 |
| 13 | g1447.t1 | CDD | cd07621 | BAR_SNX5_6 | 192 | 408 | 1.37524E-114 |
| 9 | g1447.t1 | Coils | Coil | Coil | 327 | 347 | - |
| 10 | g1447.t1 | Coils | Coil | Coil | 385 | 405 | - |
| 7 | g1447.t1 | Gene3D | G3DSA:3.30.1520.10 | PX domain | 29 | 187 | 5.1E-50 |
| 8 | g1447.t1 | Gene3D | G3DSA:1.20.1270.60 | Arfaptin | 207 | 408 | 3.3E-38 |
| 15 | g1447.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 14 | g1447.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 12 | 28 | - |
| 3 | g1447.t1 | PANTHER | PTHR45850:SF1 | SORTING NEXIN 6, ISOFORM B | 32 | 407 | 5.2E-180 |
| 4 | g1447.t1 | PANTHER | PTHR45850 | SORTING NEXIN FAMILY MEMBER | 32 | 407 | 5.2E-180 |
| 11 | g1447.t1 | PIRSF | PIRSF036924 | Snx5_Snx6 | 2 | 414 | 4.6E-195 |
| 2 | g1447.t1 | Pfam | PF00787 | PX domain | 65 | 176 | 4.0E-15 |
| 1 | g1447.t1 | Pfam | PF09325 | Vps5 C terminal like | 207 | 395 | 1.7E-10 |
| 16 | g1447.t1 | ProSiteProfiles | PS50195 | PX domain profile. | 32 | 179 | 11.383 |
| 6 | g1447.t1 | SUPERFAMILY | SSF64268 | PX domain | 38 | 176 | 3.66E-13 |
| 5 | g1447.t1 | SUPERFAMILY | SSF103657 | BAR/IMD domain-like | 207 | 406 | 9.21E-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 transcript has been annotated with K17920 (sorting nexin-5/6/32)
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.
