General information for g4570.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-3 complex subunit sigma-1.
Parent gene
- The parent gene g4570 is located on chr_2: 3267670..3268735 (+ 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_2 | g4570 | g4570.t1 | TSS | g4570.t1 | 3267583 | 3267583 |
| chr_2 | g4570 | g4570.t1 | isoform | g4570.t1 | 3267670 | 3268374 |
| chr_2 | g4570 | g4570.t1 | exon | g4570.t1.exon1 | 3267670 | 3267738 |
| chr_2 | g4570 | g4570.t1 | cds | g4570.t1.CDS1 | 3267670 | 3267738 |
| chr_2 | g4570 | g4570.t1 | exon | g4570.t1.exon2 | 3267808 | 3268197 |
| chr_2 | g4570 | g4570.t1 | cds | g4570.t1.CDS2 | 3267808 | 3268197 |
| chr_2 | g4570 | g4570.t1 | exon | g4570.t1.exon3 | 3268255 | 3268374 |
| chr_2 | g4570 | g4570.t1 | cds | g4570.t1.CDS3 | 3268255 | 3268374 |
| chr_2 | g4570 | g4570.t1 | TTS | g4570.t1 | 3268626 | 3268626 |
Sequences
>g4570.t1 Gene=g4570 Length=579
ATGATTCAAGCTATTCTTGTATTCAATAATCATGGTCGACCCAGAATCAGTAAATTTTAT
ACGTACTTTAATGAAGATCAACAACAACAGATAATAAAAGAAACATTTCAACTTGTCAGT
AAAAGAGAAGATACAGTATGCAATTTTCTTGAATATCCAGGAACATTCCATGAAATTAGT
GCAGACTGCAAATTAATTTATAGACACTATGCTACATTATATTTCGTTTTTTGCGTGGAC
AGCAGTGAAAGTGAATTAGGAATACTTGATTTAATTCAAGTATTTGTTGAGACACTTGAT
AAATGCTTTGAAAATGTTTGCGAACTTGATCTCATTTTTCATGCTGATTCTGTACATTAC
ATTTTGAATGAACTAGTTATGGGAGGAATGGTATTGCAGACAAATATGAATGAAATATTA
GCAAGAATAGAAGACCAAAATAAACTACAAAAGGCTGAAGCTGGAATTTCAACAACTTCA
GCGTCACGTGCAGTTTCTGCCATGAAATCAATAAATCTACCCCAAATTAAAGACAAAGTT
TTAGATTTTCCTGATAAATTTCGTGATTTTAAATTTTGA
>g4570.t1 Gene=g4570 Length=192
MIQAILVFNNHGRPRISKFYTYFNEDQQQQIIKETFQLVSKREDTVCNFLEYPGTFHEIS
ADCKLIYRHYATLYFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHADSVHY
ILNELVMGGMVLQTNMNEILARIEDQNKLQKAEAGISTTSASRAVSAMKSINLPQIKDKV
LDFPDKFRDFKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4570.t1 | CDD | cd14834 | AP3_sigma | 1 | 148 | 7.54541E-100 |
| 6 | g4570.t1 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 165 | 1.9E-64 |
| 2 | g4570.t1 | PANTHER | PTHR11753:SF10 | AP-3 COMPLEX SUBUNIT SIGMA-2 | 1 | 180 | 1.0E-91 |
| 3 | g4570.t1 | PANTHER | PTHR11753 | ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY | 1 | 180 | 1.0E-91 |
| 1 | g4570.t1 | Pfam | PF01217 | Clathrin adaptor complex small chain | 1 | 149 | 1.2E-49 |
| 5 | g4570.t1 | ProSitePatterns | PS00989 | Clathrin adaptor complexes small chain signature. | 65 | 75 | - |
| 4 | g4570.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 148 | 1.33E-40 |
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:0015031 | protein transport | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
- This transcript has been annotated with K12399 (AP-3 complex subunit sigma)
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.
