Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-1.

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 g7579 g7579.t7 TTS g7579.t7 24637378 24637378
chr_2 g7579 g7579.t7 isoform g7579.t7 24638061 24638778
chr_2 g7579 g7579.t7 exon g7579.t7.exon1 24638061 24638778
chr_2 g7579 g7579.t7 cds g7579.t7.CDS1 24638062 24638685
chr_2 g7579 g7579.t7 TSS g7579.t7 NA NA

Sequences

>g7579.t7 Gene=g7579 Length=718
GACTCATATGTCGGTGATGAGGCTCAAAGCAAAAGAGGTATCCTCACATTGAAATATCCA
ATTGAACACGGTATCATCACAAACTGGGACGATATGGAAAAGATCTGGCATCACACATTC
TACAATGAACTTCGTGTTGCACCAGAAGAACACCCAGTCTTGCTCACAGAAGCTCCATTG
AACCCAAAGGCTAACCGTGAGAAGATGACACAAATCATGTTCGAAACCTTCAACTCACCA
GCTATGTATGTCGCCATCCAAGCCGTTCTCTCATTGTACGCTTCAGGTCGTACCACTGGT
ATTGTTTTGGATTCAGGAGATGGTGTTTCACACACAGTCCCAATTTATGAAGGTTATGCC
TTGCCACATGCCATCCTCCGTCTTGACTTGGCTGGTCGTGACTTGACTGATTACTTGATG
AAGATCTTGACCGAACGTGGTTACTCATTCACAACCACTGCTGAACGTGAAATTGTTCGT
GATATTAAGGAAAAATTGTGCTATGTTGCTTTGGACTTTGAACAAGAAATGGCCACAGCT
GCTGCATCAACATCACTCGAGAAGTCATATGAATTGCCTGATGGTCAAGTTATCACCATC
GGTAATGAACGTTTCCGTTGCCCAGAAGCATTGTTCCAACCATCATTCTTGGGTATGGAA
TCATGCGGTATTCACGAGACCGTCTACAATTCAATCATGAAATGCGACGTTGATATCC

>g7579.t7 Gene=g7579 Length=208
MEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNSPAMYVAIQAVLS
LYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFT
TTAEREIVRDIKEKLCYVALDFEQEMATAAASTSLEKSYELPDGQVITIGNERFRCPEAL
FQPSFLGMESCGIHETVYNSIMKCDVDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7579.t7 CDD cd00012 NBD_sugar-kinase_HSP70_actin 1 100 3.16332E-15
12 g7579.t7 Gene3D G3DSA:3.30.420.40 - 1 56 2.8E-105
11 g7579.t7 Gene3D G3DSA:3.30.420.40 - 57 208 2.8E-105
10 g7579.t7 Gene3D G3DSA:3.90.640.10 Actin; Chain A 99 191 2.8E-105
2 g7579.t7 PANTHER PTHR11937:SF397 ACTIN, INDIRECT FLIGHT MUSCLE-RELATED 1 208 5.1E-145
3 g7579.t7 PANTHER PTHR11937 ACTIN 1 208 5.1E-145
6 g7579.t7 PRINTS PR00190 Actin signature 3 21 3.6E-42
7 g7579.t7 PRINTS PR00190 Actin signature 34 47 3.6E-42
5 g7579.t7 PRINTS PR00190 Actin signature 59 78 3.6E-42
4 g7579.t7 PRINTS PR00190 Actin signature 155 171 3.6E-42
1 g7579.t7 Pfam PF00022 Actin 1 208 4.4E-75
14 g7579.t7 ProSitePatterns PS01132 Actins and actin-related proteins signature. 23 35 -
15 g7579.t7 SMART SM00268 actin_3 1 208 1.7E-53
9 g7579.t7 SUPERFAMILY SSF53067 Actin-like ATPase domain 1 72 1.57E-30
8 g7579.t7 SUPERFAMILY SSF53067 Actin-like ATPase domain 66 208 1.4E-56

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed