Gene loci information

Transcript annotation

  • This transcript has been annotated as Profilin.

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_2 g4530 g4530.t30 TTS g4530.t30 3100558 3100558
chr_2 g4530 g4530.t30 isoform g4530.t30 3100666 3104763
chr_2 g4530 g4530.t30 exon g4530.t30.exon1 3100666 3101123
chr_2 g4530 g4530.t30 cds g4530.t30.CDS1 3101026 3101123
chr_2 g4530 g4530.t30 exon g4530.t30.exon2 3101205 3101367
chr_2 g4530 g4530.t30 cds g4530.t30.CDS2 3101205 3101367
chr_2 g4530 g4530.t30 exon g4530.t30.exon3 3104653 3104763
chr_2 g4530 g4530.t30 cds g4530.t30.CDS3 3104653 3104763
chr_2 g4530 g4530.t30 TSS g4530.t30 3105043 3105043

Sequences

>g4530.t30 Gene=g4530 Length=732
ATGAGTTGGCAAGATTATGTAGATAACCAATTAATAGCATCACAGTGCGTATCAAAGGCC
TGCATTTCTGGCCACGACGGAGGTATTTGGGCGAAATCAGAAGGTTTTGAGGAAGAACTC
GCCAAATTAGTACAAGGCTTTGATAAAACTGAAATTTTAACGTCAGGCGGAGTAACACTC
GCCGGACAACGTCACATTTACCTCTCTGGAACAGATCGTGTTATTCGTGCGAAGTTGGGT
AAAGTTGGTGTTCACTGTATGAAAACACAACAAGCTGTAATTGTTGCAATTTATGAAGAG
CCAGTTCAGCCACAACAGGCTGCTTCCGTCGTTGAGAAACTTGGAGACTATTTGATCACA
TGTGGTTATTAGAGGTAAGGCATCATCGCGCAAATTAGAACACACACGCATTTGTCCGCC
CAGCCAAGTCAGCACCCCCAAAATTCAATAAAAACAAAATACTATAAACACAACATCAAC
AAAACATTTGCAGAAAAGAAGAAAAAACTATCAATAATAATCGCAATTTTGCATACATTT
AAAATGAATTTTTTTTGTTTCATCGTGTGATTGATTGAAGATTTGACATTCTTCCAAGCA
CACATCAAAAAACATCCTTAAATAAAAAATATACATATTCATCTTATCCCCACAATTTAC
ATTTATATAAATACATGTATAAAAGAATATTTAAAGCTCATTTTATCTGAATGGAATTTT
TTAAATCATTCT

>g4530.t30 Gene=g4530 Length=123
MSWQDYVDNQLIASQCVSKACISGHDGGIWAKSEGFEEELAKLVQGFDKTEILTSGGVTL
AGQRHIYLSGTDRVIRAKLGKVGVHCMKTQQAVIVAIYEEPVQPQQAASVVEKLGDYLIT
CGY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4530.t30 CDD cd00148 PROF 2 123 4.67593E-48
15 g4530.t30 Gene3D G3DSA:3.30.450.30 Dynein light chain 2a 1 123 8.5E-39
2 g4530.t30 PANTHER PTHR11604 PROFILIN 1 123 3.6E-35
3 g4530.t30 PANTHER PTHR11604:SF0 PROFILIN 1 123 3.6E-35
8 g4530.t30 PRINTS PR01640 Plant profilin signature 1 12 1.1E-17
11 g4530.t30 PRINTS PR00392 Profilin signature 3 12 4.6E-19
10 g4530.t30 PRINTS PR00392 Profilin signature 18 27 4.6E-19
5 g4530.t30 PRINTS PR01640 Plant profilin signature 24 37 1.1E-17
9 g4530.t30 PRINTS PR00392 Profilin signature 57 71 4.6E-19
6 g4530.t30 PRINTS PR01640 Plant profilin signature 76 91 1.1E-17
12 g4530.t30 PRINTS PR00392 Profilin signature 92 105 4.6E-19
4 g4530.t30 PRINTS PR01640 Plant profilin signature 96 109 1.1E-17
13 g4530.t30 PRINTS PR00392 Profilin signature 105 122 4.6E-19
7 g4530.t30 PRINTS PR01640 Plant profilin signature 109 122 1.1E-17
1 g4530.t30 Pfam PF00235 Profilin 1 123 7.5E-39
17 g4530.t30 ProSitePatterns PS00414 Profilin signature. 1 8 -
18 g4530.t30 SMART SM00392 prof_2 1 123 2.7E-53
14 g4530.t30 SUPERFAMILY SSF55770 Profilin (actin-binding protein) 2 123 3.53E-37

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

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.

Raw TPM values