General information for g392.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cofilin/actin-depolymerizing factor-like protein.
Parent gene
- The parent gene g392 is located on chr_3: 3150070..3151159 (+ 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 | g392 | g392.t1 | TSS | g392.t1 | 3149979 | 3149979 |
| chr_3 | g392 | g392.t1 | isoform | g392.t1 | 3150070 | 3150674 |
| chr_3 | g392 | g392.t1 | exon | g392.t1.exon1 | 3150070 | 3150088 |
| chr_3 | g392 | g392.t1 | cds | g392.t1.CDS1 | 3150070 | 3150088 |
| chr_3 | g392 | g392.t1 | exon | g392.t1.exon2 | 3150247 | 3150674 |
| chr_3 | g392 | g392.t1 | cds | g392.t1.CDS2 | 3150247 | 3150674 |
| chr_3 | g392 | g392.t1 | TTS | g392.t1 | 3151016 | 3151016 |
Sequences
>g392.t1 Gene=g392 Length=447
ATGGCTAGCGGTGTTGAAGTTAATGATAAATGCAAAATTATCTTTGAGGAGATTAAAAAA
GACAAGAAGCATCGCTATGTGATCTTCAATATTGTGGACGAGAAACAAATTGATGTAGAA
GTGATTGGTGACCGTGATGCAGAATACGACTCGTTTTTGGAAGATTTGCAAAAGGGCGGT
ACTGGTGAATGTCGCTATGGACTTTTTGATTTTGAATATATGCATCAGCATCAAGGTACT
ACTGAATCATCGAAGAAACAAAAACTCTTTCTTCTGTTGTGGTGCCCAGACACAGCTAAA
ATCAAAATGAAGATGCTTTATGCTTCATCATTTGACGCACTCAAAAAGTCATTGGTTGGT
GTGCAAAAATACATTCAGGCTTCAGATTTGTCGGAAGCATCAAAGGAGTCAGTAGAAGAA
AAGTTGCGCGCAACTGATCGCGTCTAA
>g392.t1 Gene=g392 Length=148
MASGVEVNDKCKIIFEEIKKDKKHRYVIFNIVDEKQIDVEVIGDRDAEYDSFLEDLQKGG
TGECRYGLFDFEYMHQHQGTTESSKKQKLFLLLWCPDTAKIKMKMLYASSFDALKKSLVG
VQKYIQASDLSEASKESVEEKLRATDRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g392.t1 | CDD | cd11286 | ADF_cofilin_like | 3 | 142 | 0.0000000 |
| 8 | g392.t1 | Gene3D | G3DSA:3.40.20.10 | Severin | 1 | 148 | 0.0000000 |
| 2 | g392.t1 | PANTHER | PTHR11913:SF12 | COFILIN/ACTIN-DEPOLYMERIZING FACTOR HOMOLOG-RELATED | 2 | 143 | 0.0000000 |
| 3 | g392.t1 | PANTHER | PTHR11913 | COFILIN-RELATED | 2 | 143 | 0.0000000 |
| 6 | g392.t1 | PRINTS | PR00006 | Cofilin/destrin family signature | 6 | 30 | 0.0000002 |
| 5 | g392.t1 | PRINTS | PR00006 | Cofilin/destrin family signature | 90 | 111 | 0.0000002 |
| 4 | g392.t1 | PRINTS | PR00006 | Cofilin/destrin family signature | 112 | 128 | 0.0000002 |
| 1 | g392.t1 | Pfam | PF00241 | Cofilin/tropomyosin-type actin-binding protein | 11 | 141 | 0.0000000 |
| 11 | g392.t1 | ProSiteProfiles | PS51263 | ADF-H domain profile. | 2 | 143 | 32.8660000 |
| 10 | g392.t1 | SMART | SM00102 | adf_2 | 9 | 143 | 0.0000000 |
| 7 | g392.t1 | SUPERFAMILY | SSF55753 | Actin depolymerizing proteins | 1 | 143 | 0.0000000 |
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:0003779 | actin binding | MF |
| GO:0015629 | actin cytoskeleton | CC |
| GO:0030042 | actin filament depolymerization | BP |
KEGG
Orthology
- This transcript has been annotated with K05765 (cofilin)
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.
