General information for g4969.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AP-1 complex subunit sigma-2.
Parent gene
- The parent gene g4969 is located on chr_2: 6208054..6209285 (- 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 | g4969 | g4969.t1 | TTS | g4969.t1 | 6203621 | 6203621 |
| chr_2 | g4969 | g4969.t1 | isoform | g4969.t1 | 6203807 | 6209196 |
| chr_2 | g4969 | g4969.t1 | exon | g4969.t1.exon1 | 6203807 | 6203851 |
| chr_2 | g4969 | g4969.t1 | cds | g4969.t1.CDS1 | 6203807 | 6203851 |
| chr_2 | g4969 | g4969.t1 | exon | g4969.t1.exon2 | 6208512 | 6208649 |
| chr_2 | g4969 | g4969.t1 | cds | g4969.t1.CDS2 | 6208512 | 6208649 |
| chr_2 | g4969 | g4969.t1 | exon | g4969.t1.exon3 | 6208708 | 6208816 |
| chr_2 | g4969 | g4969.t1 | cds | g4969.t1.CDS3 | 6208708 | 6208816 |
| chr_2 | g4969 | g4969.t1 | exon | g4969.t1.exon4 | 6208870 | 6209048 |
| chr_2 | g4969 | g4969.t1 | cds | g4969.t1.CDS4 | 6208870 | 6209048 |
| chr_2 | g4969 | g4969.t1 | exon | g4969.t1.exon5 | 6209194 | 6209196 |
| chr_2 | g4969 | g4969.t1 | cds | g4969.t1.CDS5 | 6209194 | 6209196 |
| chr_2 | g4969 | g4969.t1 | TSS | g4969.t1 | 6209271 | 6209271 |
Sequences
>g4969.t1 Gene=g4969 Length=474
ATGATGCAATTTATGTTATTATTTAGCCGACAAGGCAAATTAAGATTACAAAAGTGGTAT
GTAGCTCATCAAGATAAAGTAAAGAAGAAGATTACAAGAGAATTGATTTCTACAATACTT
GCTCGCAAGCCGAAGATGTGCTCGTTTTTAGAGTACAAAGAATCTAAAATTGTGTATAAG
AGATATGCAAGTTTATATTTCTGCTGTGCAGTTGAGCAAGAAGACAATGAATTATTGACG
CTTGAAATCATCCATCGGTACGTGGAACTTTTAGACAAATACTTTGGAAGCGTCTGTGAA
TTAGATATCATCTTCAATTTTGAAAAGGCATATTTTATTCTCGATGAGCTATTGGTTGGC
GGTGAGATACAAGAAACATCTAAGAAAAATGTTTTGAAGGCAATTGCAGCACAAGATGTC
TTGCAAGAGGATGAAACGCCTCAAGGATTTTTCGAAGATCATGGACTTGGTTAA
>g4969.t1 Gene=g4969 Length=157
MMQFMLLFSRQGKLRLQKWYVAHQDKVKKKITRELISTILARKPKMCSFLEYKESKIVYK
RYASLYFCCAVEQEDNELLTLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDELLVG
GEIQETSKKNVLKAIAAQDVLQEDETPQGFFEDHGLG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4969.t1 | CDD | cd14831 | AP1_sigma | 3 | 145 | 7.88313E-102 |
| 6 | g4969.t1 | Gene3D | G3DSA:3.30.450.60 | - | 1 | 155 | 4.0E-61 |
| 2 | g4969.t1 | PANTHER | PTHR11753 | ADAPTOR COMPLEXES SMALL SUBUNIT FAMILY | 2 | 146 | 1.1E-87 |
| 3 | g4969.t1 | PANTHER | PTHR11753:SF45 | AP-1 COMPLEX SUBUNIT SIGMA-2 | 2 | 146 | 1.1E-87 |
| 7 | g4969.t1 | PIRSF | PIRSF015588 | AP_complex_sigma | 1 | 150 | 7.5E-68 |
| 1 | g4969.t1 | Pfam | PF01217 | Clathrin adaptor complex small chain | 1 | 140 | 2.0E-57 |
| 5 | g4969.t1 | ProSitePatterns | PS00989 | Clathrin adaptor complexes small chain signature. | 57 | 67 | - |
| 4 | g4969.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 140 | 6.87E-45 |
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 K12394 (AP-1 complex subunit sigma 1/2)
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.
