Gene loci information

Transcript annotation

  • This transcript has been annotated as Actin, muscle.

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 g13723 g13723.t13 isoform g13723.t13 32067408 32069168
chr_1 g13723 g13723.t13 exon g13723.t13.exon1 32067408 32067472
chr_1 g13723 g13723.t13 TSS g13723.t13 32067418 32067418
chr_1 g13723 g13723.t13 exon g13723.t13.exon2 32068025 32069168
chr_1 g13723 g13723.t13 cds g13723.t13.CDS1 32068608 32069168
chr_1 g13723 g13723.t13 TTS g13723.t13 32069665 32069665

Sequences

>g13723.t13 Gene=g13723 Length=1209
AAAAGTCGTTTAGTTAAAGTGTACAGATCGTTTCTGGTGGCTTCAGTTTCTTGTAGTGAA
GGTTCTAAACTCCATTCAAAATGTGTGATGATGATGTTGCTGCATTGGTCGTTGACAATG
GCTCAGGAATGTGCAAAGCTGGCTTCGCTGGTGATGACGCTCCACGTGCTGTCTTCCCAT
CAATCGTAGGTCGCCCACGTCATCAAGGTGTTATGGTCGGTATGGGTCAAAAGGACTCAT
ATGTTGGTGATGAGGCCCAAAGCAAAGAGGTATCCTTACCTTGAAATACCCAATTGAGCA
CGGTATCATCACAAACTGGGATGATATGGAGAAGATCTGGCATCACACTTTCTACAATGA
ACTTCGCGTTGCCCCAGAAGAGCACCCAGTCTTGCTCACAGAAGCTCCATTGAACCCAAA
GGCTAACCGCGAGAAGATGACACAAATCATGTTTGAAACATTCAACTCACCAGCTATGTA
TGTTGCCATCCAAGCCGTTCTCTCATTGTACGCCTCAGGTCGTACCACCGGTATTGTTTT
GGATTCAGGAGATGTGTCTCACACACAGTCCCAATTTATGAAGGTTATGCTTTGCCACAT
GCCATCCTCCGTCTTGACTTGGCCGGTCGCGACTTGACTGACTACTTGATGAAGATCTTG
ACCGAACGCGGTTACTCATTCGTCACAACAGCTGAACGTGAAATCGTTCGTGACATCAAG
GAAAAGTTGTGCTATGTTGCATTGGACTTCGAACAAGAAATGGCCACCGCTGCTGCCTCA
ACCTCACTCGAGAAGTCATATGAATTGCCTGATGGTCAAGTTATCACCATCGGTAACGAA
CGTTTCCGTTGCCCAGAATCATTGTTCCAACCATCATTCTTGGGTATGGAATCATGCGGT
ATTCACGAAACCGTCTACAATTCAATCATGAAGTGCGATGTTGATATCCGTAAGGACTTG
TACGCCAACAACGTCTTATCAGGTGGCACAACAATGTACCCAGGTATTGCCGATCGTATG
CAAAAGGAAATGACTGCCCTCGCTCCATCAACAATCAAGATCAAGATCATTGCTCCACCA
GAACGTAAATACTCAGTCTGGATCGGAGGTTCAATCTTGGCATCACTCTCAACCTTCCAG
CAGATGTGGATCTCAAAGGAAGAATACGACGAATCAGGCCCAGGCATTGTTCACCGCAAG
TGCTTCTAA

>g13723.t13 Gene=g13723 Length=186
MKILTERGYSFVTTAEREIVRDIKEKLCYVALDFEQEMATAAASTSLEKSYELPDGQVIT
IGNERFRCPESLFQPSFLGMESCGIHETVYNSIMKCDVDIRKDLYANNVLSGGTTMYPGI
ADRMQKEMTALAPSTIKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKEEYDESGPGI
VHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13723.t13 Gene3D G3DSA:3.90.640.10 Actin; Chain A 1 82 4.2E-79
8 g13723.t13 Gene3D G3DSA:3.30.420.40 - 83 149 4.2E-79
9 g13723.t13 Gene3D G3DSA:3.30.420.40 - 150 177 4.2E-79
2 g13723.t13 PANTHER PTHR11937:SF397 ACTIN, INDIRECT FLIGHT MUSCLE-RELATED 1 185 2.0E-118
3 g13723.t13 PANTHER PTHR11937 ACTIN 1 185 2.0E-118
1 g13723.t13 Pfam PF00022 Actin 6 186 5.1E-69
6 g13723.t13 ProSitePatterns PS00432 Actins signature 2. 167 175 -
5 g13723.t13 SMART SM00268 actin_3 1 186 1.7E-22
4 g13723.t13 SUPERFAMILY SSF53067 Actin-like ATPase domain 1 186 2.22E-77

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