General information for g7267.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-3 complex subunit sigma-2.
Parent gene
- The parent gene g7267 is located on chr_2: 22557026..22557803 (+ 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 | g7267 | g7267.t4 | TSS | g7267.t4 | 22556154 | 22556154 |
| chr_2 | g7267 | g7267.t4 | isoform | g7267.t4 | 22556210 | 22557026 |
| chr_2 | g7267 | g7267.t4 | exon | g7267.t4.exon1 | 22556210 | 22556230 |
| chr_2 | g7267 | g7267.t4 | exon | g7267.t4.exon2 | 22556350 | 22556448 |
| chr_2 | g7267 | g7267.t4 | cds | g7267.t4.CDS1 | 22556380 | 22556448 |
| chr_2 | g7267 | g7267.t4 | exon | g7267.t4.exon3 | 22556508 | 22557026 |
| chr_2 | g7267 | g7267.t4 | cds | g7267.t4.CDS2 | 22556508 | 22557026 |
| chr_2 | g7267 | g7267.t4 | TTS | g7267.t4 | 22557161 | 22557161 |
Sequences
>g7267.t4 Gene=g7267 Length=639
CGGTATTAATAGCTGTACATTAACAAATCGCACAAAAACTAATTTTTTAAAATGATTAAT
GCAATTCTTGTTTTCAATAATTATGGAAAGCCAAGATTATCAAGATTTTATCAATATTTT
ACAATCGAAGAGCAGCAACAAATCATAAGTGAAACTTTTCATCTCTTGTCAAAACGAGAT
GATCAAACATGTAATTTTCTTGAACTTCCTTCAACTTCAATAATTTGCATGCGTTCGACA
GAAAATTGCAAATTAATTTATCGTCATTATGCGACTCTCTTCTTTGTTTTTTGTGTCGAT
GCTGCAGAATCTGAATTAGGAATTCTTGATTTGATTCAAGTTTTTGTTGAATCACTTGAT
CGCTCATTCTCAAATGTCTGTGAATTGGATCTGATTTTTAATAGTGATGCAATCAACTAT
TTATTGGATGAAATTGTCATGTCAGGTTTAGTTATAGAGACTAACATTAACAATATCATA
TCGCGATTTGAAGAACAAAATAGAATTGCTAAAGTTGAAACTTCACCAGCATCGGTTAAA
GCAACATCAGCAGTTTCAGCAATTAAGAACATGAATTTGCCTCAATTAAGAGATAGAGTT
AAAGATTTGCCAAACACATTTAAAGACTTGAAATTCTGA
>g7267.t4 Gene=g7267 Length=195
MINAILVFNNYGKPRLSRFYQYFTIEEQQQIISETFHLLSKRDDQTCNFLELPSTSIICM
RSTENCKLIYRHYATLFFVFCVDAAESELGILDLIQVFVESLDRSFSNVCELDLIFNSDA
INYLLDEIVMSGLVIETNINNIISRFEEQNRIAKVETSPASVKATSAVSAIKNMNLPQLR
DRVKDLPNTFKDLKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7267.t4 | CDD | cd14834 | AP3_sigma | 1 | 151 | 0 |
| 5 | g7267.t4 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 168 | 0 |
| 2 | g7267.t4 | PANTHER | PTHR11753:SF10 | AP-3 COMPLEX SUBUNIT SIGMA-2 | 1 | 183 | 0 |
| 3 | g7267.t4 | PANTHER | PTHR11753 | ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY | 1 | 183 | 0 |
| 6 | g7267.t4 | PIRSF | PIRSF015588 | AP_complex_sigma | 1 | 163 | 0 |
| 1 | g7267.t4 | Pfam | PF01217 | Clathrin adaptor complex small chain | 1 | 151 | 0 |
| 4 | g7267.t4 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 149 | 0 |
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:0015031 | protein 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.
