General information for g392.t3
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.t3 | TSS | g392.t3 | 3149979 | 3149979 |
| chr_3 | g392 | g392.t3 | isoform | g392.t3 | 3150070 | 3151159 |
| chr_3 | g392 | g392.t3 | exon | g392.t3.exon1 | 3150070 | 3150079 |
| chr_3 | g392 | g392.t3 | cds | g392.t3.CDS1 | 3150070 | 3150079 |
| chr_3 | g392 | g392.t3 | exon | g392.t3.exon2 | 3150247 | 3151159 |
| chr_3 | g392 | g392.t3 | cds | g392.t3.CDS2 | 3150247 | 3150674 |
| chr_3 | g392 | g392.t3 | TTS | g392.t3 | NA | NA |
Sequences
>g392.t3 Gene=g392 Length=923
ATGGCTAGCGTTAATGATAAATGCAAAATTATCTTTGAGGAGATTAAAAAAGACAAGAAG
CATCGCTATGTGATCTTCAATATTGTGGACGAGAAACAAATTGATGTAGAAGTGATTGGT
GACCGTGATGCAGAATACGACTCGTTTTTGGAAGATTTGCAAAAGGGCGGTACTGGTGAA
TGTCGCTATGGACTTTTTGATTTTGAATATATGCATCAGCATCAAGGTACTACTGAATCA
TCGAAGAAACAAAAACTCTTTCTTCTGTTGTGGTGCCCAGACACAGCTAAAATCAAAATG
AAGATGCTTTATGCTTCATCATTTGACGCACTCAAAAAGTCATTGGTTGGTGTGCAAAAA
TACATTCAGGCTTCAGATTTGTCGGAAGCATCAAAGGAGTCAGTAGAAGAAAAGTTGCGC
GCAACTGATCGCGTCTAAGTTCCATATTTCCATAATTCTGATAATAATAATGAGAGAGGA
TTGATTGATTGATTTTCAAGCTTTTTCTTCCTACTAAAATATATTACTAAATACATACTA
CTTACTCGCTACACACATATATAATTATTCCAAAAAAAAAAAAATCATTTTTCCTTTACG
TGAAACTGAGTTACAGTATCAAATTGTGCGTGTGAAAAAAAGTGGATAGTATGCATCATT
TGATGTTGCTTCCATTTAAGCCAATTCATTTTTTTTTTGTATTTAATCCCAGATAAGGAA
TGTCTTGAATTTAAAAATTCTTTTTTCCATTTAATAAAAAAATCATGCATTTTGATTCAT
AAAACAACTTTTTTTTATTTTTGAGGCATTTGTGTGTAATTTTGGTATGATTCATAAGTT
AATAATAGCTCTTACAATAAAAATGAGTGTGATGGACAAAATTAAGTGATGCATGTGTGA
ATGAATATGATGCAGAAAAAAGT
>g392.t3 Gene=g392 Length=145
MASVNDKCKIIFEEIKKDKKHRYVIFNIVDEKQIDVEVIGDRDAEYDSFLEDLQKGGTGE
CRYGLFDFEYMHQHQGTTESSKKQKLFLLLWCPDTAKIKMKMLYASSFDALKKSLVGVQK
YIQASDLSEASKESVEEKLRATDRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g392.t3 | CDD | cd11286 | ADF_cofilin_like | 2 | 139 | 0.00 |
| 6 | g392.t3 | Gene3D | G3DSA:3.40.20.10 | Severin | 2 | 145 | 0.00 |
| 2 | g392.t3 | PANTHER | PTHR11913:SF12 | COFILIN/ACTIN-DEPOLYMERIZING FACTOR HOMOLOG-RELATED | 3 | 140 | 0.00 |
| 3 | g392.t3 | PANTHER | PTHR11913 | COFILIN-RELATED | 3 | 140 | 0.00 |
| 1 | g392.t3 | Pfam | PF00241 | Cofilin/tropomyosin-type actin-binding protein | 8 | 138 | 0.00 |
| 7 | g392.t3 | ProSiteProfiles | PS51263 | ADF-H domain profile. | 1 | 140 | 33.13 |
| 5 | g392.t3 | SMART | SM00102 | adf_2 | 6 | 140 | 0.00 |
| 4 | g392.t3 | SUPERFAMILY | SSF55753 | Actin depolymerizing proteins | 3 | 140 | 0.00 |
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.
