Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t23 isoform g4530.t23 3100553 3104763
chr_2 g4530 g4530.t23 exon g4530.t23.exon1 3100553 3101132
chr_2 g4530 g4530.t23 TTS g4530.t23 3100558 3100558
chr_2 g4530 g4530.t23 cds g4530.t23.CDS1 3101026 3101132
chr_2 g4530 g4530.t23 exon g4530.t23.exon2 3101232 3101376
chr_2 g4530 g4530.t23 cds g4530.t23.CDS2 3101232 3101376
chr_2 g4530 g4530.t23 exon g4530.t23.exon3 3104653 3104763
chr_2 g4530 g4530.t23 cds g4530.t23.CDS3 3104653 3104763
chr_2 g4530 g4530.t23 TSS g4530.t23 3105043 3105043

Sequences

>g4530.t23 Gene=g4530 Length=836
ATGAGTTGGCAAGATTATGTAGATAACCAATTAATAGCATCACAGTGCGTATCAAAGGCC
TGCATTTCTGGCCACGACGGAGGTATTTGGGCGAAATCAGAAGGTTTTGAGGTAACAAAG
GAAGAACTCGCCAAATTAGTACAAGGCTTTGATAAAACTGAAATTTTAACGTCAGGCGGA
GTAACACTCGCCGGACAACGTCACATTTACCTCTCTGGAACAGATCGTGTTATTCGTGCG
AAGTTGGGTAAAGTTGCATACGCAGCTGTAATTGTTGCAATTTATGAAGAGCCAGTTCAG
CCACAACAGGCTGCTTCCGTCGTTGAGAAACTTGGAGACTATTTGATCACATGTGGTTAT
TAGAGGTAAGGCATCATCGCGCAAATTAGAACACACACGCATTTGTCCGCCCAGCCAAGT
CAGCACCCCCAAAATTCAATAAAAACAAAATACTATAAACACAACATCAACAAAACATTT
GCAGAAAAGAAGAAAAAACTATCAATAATAATCGCAATTTTGCATACATTTAAAATGAAT
TTTTTTTGTTTCATCGTGTGATTGATTGAAGATTTGACATTCTTCCAAGCACACATCAAA
AAACATCCTTAAATAAAAAATATACATATTCATCTTATCCCCACAATTTACATTTATATA
AATACATGTATAAAAGAATATTTAAAGCTCATTTTATCTGAATGGAATTTTTTAAATCAT
TCTCTTTTCATTTTGAGTTTTTCGTATGAGATTTTTGAATTTTTTTCTATGTATAACCAA
ATTCTCGTGAATAAATTGAAATTCGATTCATTTTTGTGATCGCTTAGAAAGAAAAC

>g4530.t23 Gene=g4530 Length=120
MSWQDYVDNQLIASQCVSKACISGHDGGIWAKSEGFEVTKEELAKLVQGFDKTEILTSGG
VTLAGQRHIYLSGTDRVIRAKLGKVAYAAVIVAIYEEPVQPQQAASVVEKLGDYLITCGY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g4530.t23 CDD cd00148 PROF 2 120 3.86104E-41
13 g4530.t23 Gene3D G3DSA:3.30.450.30 Dynein light chain 2a 1 120 2.0E-33
2 g4530.t23 PANTHER PTHR11604 PROFILIN 1 120 1.7E-30
3 g4530.t23 PANTHER PTHR11604:SF0 PROFILIN 1 120 1.7E-30
6 g4530.t23 PRINTS PR01640 Plant profilin signature 1 12 2.0E-10
10 g4530.t23 PRINTS PR00392 Profilin signature 3 12 3.4E-18
9 g4530.t23 PRINTS PR00392 Profilin signature 18 27 3.4E-18
5 g4530.t23 PRINTS PR01640 Plant profilin signature 24 37 2.0E-10
7 g4530.t23 PRINTS PR00392 Profilin signature 36 56 3.4E-18
8 g4530.t23 PRINTS PR00392 Profilin signature 89 102 3.4E-18
11 g4530.t23 PRINTS PR00392 Profilin signature 102 119 3.4E-18
4 g4530.t23 PRINTS PR01640 Plant profilin signature 106 119 2.0E-10
1 g4530.t23 Pfam PF00235 Profilin 1 120 1.6E-34
15 g4530.t23 ProSitePatterns PS00414 Profilin signature. 1 8 -
16 g4530.t23 SMART SM00392 prof_2 1 120 5.7E-46
12 g4530.t23 SUPERFAMILY SSF55770 Profilin (actin-binding protein) 2 120 1.57E-33

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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