General information for g10729.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-2 complex subunit sigma.
Parent gene
- The parent gene g10729 is located on chr_1: 11615180..11616994 (+ 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_1 | g10729 | g10729.t1 | TSS | g10729.t1 | 11614560 | 11614560 |
| chr_1 | g10729 | g10729.t1 | isoform | g10729.t1 | 11614633 | 11615180 |
| chr_1 | g10729 | g10729.t1 | exon | g10729.t1.exon1 | 11614633 | 11614635 |
| chr_1 | g10729 | g10729.t1 | cds | g10729.t1.CDS1 | 11614633 | 11614635 |
| chr_1 | g10729 | g10729.t1 | exon | g10729.t1.exon2 | 11614703 | 11614852 |
| chr_1 | g10729 | g10729.t1 | cds | g10729.t1.CDS2 | 11614703 | 11614852 |
| chr_1 | g10729 | g10729.t1 | exon | g10729.t1.exon3 | 11614905 | 11615180 |
| chr_1 | g10729 | g10729.t1 | cds | g10729.t1.CDS3 | 11614905 | 11615180 |
| chr_1 | g10729 | g10729.t1 | TTS | g10729.t1 | 11615401 | 11615401 |
Sequences
>g10729.t1 Gene=g10729 Length=429
ATGATTCGTTTTATTTTGATTCAAAACCGTGCAGGAAAAACTAGATTAGCAAAATGGTAT
ATGCAATTCGATGACGATGAAAAACAAAAATTAATTGAAGAAGTTCATGCTGTAGTCACT
GTCAGAGATGCTAAACATACCAATTTTGTTGAATTTCGCAACTTTAAGATTGTCTATAGA
CGATATGCTGGATTATATTTCTGTATATGTGTTGACGTTAATGATAACAACTTGTGCTAT
CTCGAAGCGATTCACAATTTCGTGGAAGTTTTAAATGAGTATTTCCATAATGTTTGTGAA
TTGGATCTGGTATTCAATTTTTATAAAGTTTATACTGTTGTCGATGAGATGTTTTTAGCA
GGCGAGATTAGAGAGACTTCACAAACAAAAGTCCTCAAGCAGCTGCTTACACTCAATTCA
TTAGACTAA
>g10729.t1 Gene=g10729 Length=142
MIRFILIQNRAGKTRLAKWYMQFDDDEKQKLIEEVHAVVTVRDAKHTNFVEFRNFKIVYR
RYAGLYFCICVDVNDNNLCYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMFLA
GEIRETSQTKVLKQLLTLNSLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10729.t1 | CDD | cd14833 | AP2_sigma | 1 | 141 | 2.80548E-92 |
| 6 | g10729.t1 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 142 | 2.9E-56 |
| 2 | g10729.t1 | PANTHER | PTHR11753:SF6 | AP-2 COMPLEX SUBUNIT SIGMA | 2 | 141 | 1.9E-77 |
| 3 | g10729.t1 | PANTHER | PTHR11753 | ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY | 2 | 141 | 1.9E-77 |
| 7 | g10729.t1 | PIRSF | PIRSF015588 | AP_complex_sigma | 1 | 142 | 7.9E-64 |
| 1 | g10729.t1 | Pfam | PF01217 | Clathrin adaptor complex small chain | 1 | 141 | 3.8E-62 |
| 5 | g10729.t1 | ProSitePatterns | PS00989 | Clathrin adaptor complexes small chain signature. | 57 | 67 | - |
| 4 | g10729.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 136 | 2.61E-43 |
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:0030117 | membrane coat | CC |
| GO:0072583 | clathrin-dependent endocytosis | BP |
| GO:0035615 | clathrin adaptor activity | MF |
| GO:0030122 | AP-2 adaptor complex | CC |
| GO:0015031 | protein transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K11827 (AP-2 complex subunit sigma-1)
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.
