Gene loci information

Transcript annotation

  • This transcript has been annotated as Cofilin/actin-depolymerizing factor-like protein.

Parent gene

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_4 g16136 g16136.t3 isoform g16136.t3 8334068 8342707
chr_4 g16136 g16136.t3 exon g16136.t3.exon1 8334068 8334200
chr_4 g16136 g16136.t3 exon g16136.t3.exon2 8338172 8338589
chr_4 g16136 g16136.t3 cds g16136.t3.CDS1 8338443 8338589
chr_4 g16136 g16136.t3 exon g16136.t3.exon3 8338651 8338947
chr_4 g16136 g16136.t3 cds g16136.t3.CDS2 8338651 8338947
chr_4 g16136 g16136.t3 exon g16136.t3.exon4 8342705 8342707
chr_4 g16136 g16136.t3 cds g16136.t3.CDS3 8342705 8342707
chr_4 g16136 g16136.t3 TSS g16136.t3 8342954 8342954
chr_4 g16136 g16136.t3 TTS g16136.t3 NA NA

Sequences

>g16136.t3 Gene=g16136 Length=851
ATGGCTTCCGGAGTAACTGTCTCAGATGTTTGTAAGACAACATATGAAGAAATTAAGAAG
GACAAAAAACATCGCTATGTAATTTTTTACATTCGTGATGAGAAGCAAATTGATGTGGAA
GTGATTGGTGAACGTAATGCAGAATATGATTCGTTCCTTGAAGATATTCAAAAAGGCGGT
CCAGGTGAATGCCGATATGGACTCTTTGATTTTGAGTATATGCATCAATGTCAAGGCACC
TCTGAGAGTTCCAAGAAGCAAAAATTATTTTTAATGTCCTGGTGTCCAGATACTGCTAAA
GTCAAGAAGAAGATGTTGTACTCAAGCTCATTTGATGCATTGAAAAAGTCACTTGTAGGT
GTGCAAAAATACATTCAAGCTACAGACTTATCAGAGGCCTCACGTGAAGCTGTTGAAGAA
AAATTGCGCTCTACTGATCGCAACTAAATTCTCCTTCATCTCCATCAAAAAAATTCTTTA
CATCTCTCTCTTTTTTGAATTATTATTATTATTATTTTGCAACAATTACATCAAATTTAT
CTATTCATTTATAAAATGTGTCAACAAATTAATTTTCTCTCCCCATTTTATTTGTCTCAT
TTTTTAAATAAAAAAAATAATTAAAGTAATTAATTATTGATTAAAATAAACTCAAAAACT
GAAAAAGAACATTTAAATAAAAATGATTTTTTAAGTTTTATTAGCTGAAATAAAATTTAA
ATTATTTCGATCATAAACTCCCATCTGATCTCGTATAAAATAATGCATGGCACGAAAAGC
AATATTGAATTCAACACTGACTTGAGGATTGATATTTGGATCGTAGCATTTTGTTGATGG
TATTTTGAAAT

>g16136.t3 Gene=g16136 Length=148
MASGVTVSDVCKTTYEEIKKDKKHRYVIFYIRDEKQIDVEVIGERNAEYDSFLEDIQKGG
PGECRYGLFDFEYMHQCQGTSESSKKQKLFLMSWCPDTAKVKKKMLYSSSFDALKKSLVG
VQKYIQATDLSEASREAVEEKLRSTDRN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16136.t3 CDD cd11286 ADF_cofilin_like 3 142 1.9801E-58
6 g16136.t3 Coils Coil Coil 135 148 -
5 g16136.t3 Gene3D G3DSA:3.40.20.10 Severin 1 148 8.6E-53
2 g16136.t3 PANTHER PTHR11913:SF12 COFILIN/ACTIN-DEPOLYMERIZING FACTOR HOMOLOG-RELATED 2 143 1.8E-40
3 g16136.t3 PANTHER PTHR11913 COFILIN-RELATED 2 143 1.8E-40
1 g16136.t3 Pfam PF00241 Cofilin/tropomyosin-type actin-binding protein 11 141 4.4E-33
9 g16136.t3 ProSiteProfiles PS51263 ADF-H domain profile. 4 143 33.393
8 g16136.t3 SMART SM00102 adf_2 9 143 4.1E-52
4 g16136.t3 SUPERFAMILY SSF55753 Actin depolymerizing proteins 1 144 5.95E-38

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

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. There were no conditions that were differentially expressed