Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin-42A.

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_1 g14309 g14309.t24 TTS g14309.t24 36551672 36551672
chr_1 g14309 g14309.t24 isoform g14309.t24 36552428 36555404
chr_1 g14309 g14309.t24 exon g14309.t24.exon1 36552428 36553070
chr_1 g14309 g14309.t24 cds g14309.t24.CDS1 36552430 36553062
chr_1 g14309 g14309.t24 exon g14309.t24.exon2 36555209 36555404
chr_1 g14309 g14309.t24 TSS g14309.t24 36555404 36555404

Sequences

>g14309.t24 Gene=g14309 Length=839
ATCAATGAAAGTCTGAAAGTCTAGCTGTATAGACGAAAAAATAGTAATTTTAGTAATAAA
AAGCTAAGAAACTTGAAGTTTTTTGAAACCCCAAGGATAAATTGAATAAGCTTCAACAAA
TTTGTTAAACTCTCATAGTTTAGTGGAATAATTTATTATATTAATAAACACTTTTTAAAT
AAACCAAATGTAAGTAAAATCAAAATGTGTGACGAAGAAGTTGCTGCATTGGTCGTTGAC
AATGGATCAGGAATGTGCAAAGCCGGTTTTGCTGGTGATGATGCACCACGTGCCGTTTTC
CCATCAATTGTCGGTCGTCCACGTCATCAAGGCGTTATGGTCGGTATGGGACAAAAGGAC
TCATATGTTGGTGATGAGGCTCAAAGCAAAAGAGGTATTCTTACCTTGAAATATCCAATT
GAACACGGTATTGTTACAAACTGGGATGATATGGAAAAGATCTGGCATCATACTTTCTAC
AATGAACTCCGTGTTGCACCTGAAGAACATCCAGTCTTGCTTACCGAAGCTCCATTAAAT
CCAAAAGCAAATCGTGAAAAGATGACACAAATTATGTTCGAGACATTCAACACACCAGCT
ATGTATGTTGCAATTCAAGCTGTCCTCTCATTGTATGCCTCAGGTCGTACAACTGGTATT
GTTTTGGATTCTGGTGATGGTGTTTCACACACAGTTCCAATTTACGAAGGTTATGCTTTG
CCACATGCTATCCTTCGTCTTGATTTGGCCGGTCGTGATTTGACAGATTATTTGATGAAA
ATCTTAACCGAACGTGGATACTCATTCACAACCACTGCCGAACGTGAAATTGTTCGTGA

>g14309.t24 Gene=g14309 Length=211
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDYLMKILTERGYSFTTTAEREIVR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g14309.t24 CDD cd00012 NBD_sugar-kinase_HSP70_actin 9 182 1.06674E-19
11 g14309.t24 Gene3D G3DSA:2.30.36.70 Actin; Chain A 35 72 2.5E-29
12 g14309.t24 Gene3D G3DSA:3.30.420.40 - 154 211 8.9E-13
2 g14309.t24 PANTHER PTHR11937:SF162 ACTIN, INDIRECT FLIGHT MUSCLE-LIKE PROTEIN 1 211 4.7E-145
3 g14309.t24 PANTHER PTHR11937 ACTIN 1 211 4.7E-145
6 g14309.t24 PRINTS PR00190 Actin signature 27 36 1.2E-47
7 g14309.t24 PRINTS PR00190 Actin signature 50 61 1.2E-47
8 g14309.t24 PRINTS PR00190 Actin signature 62 84 1.2E-47
5 g14309.t24 PRINTS PR00190 Actin signature 116 129 1.2E-47
4 g14309.t24 PRINTS PR00190 Actin signature 141 160 1.2E-47
1 g14309.t24 Pfam PF00022 Actin 4 211 6.4E-78
15 g14309.t24 ProSitePatterns PS00406 Actins signature 1. 54 64 -
14 g14309.t24 ProSitePatterns PS01132 Actins and actin-related proteins signature. 105 117 -
16 g14309.t24 SMART SM00268 actin_3 6 211 8.2E-57
10 g14309.t24 SUPERFAMILY SSF53067 Actin-like ATPase domain 5 154 5.83E-67
9 g14309.t24 SUPERFAMILY SSF53067 Actin-like ATPase domain 147 211 1.77E-21

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.

Raw TPM values