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.t12 isoform g13723.t12 32067408 32069168
chr_1 g13723 g13723.t12 exon g13723.t12.exon1 32067408 32067472
chr_1 g13723 g13723.t12 TSS g13723.t12 32067418 32067418
chr_1 g13723 g13723.t12 exon g13723.t12.exon2 32068038 32069168
chr_1 g13723 g13723.t12 cds g13723.t12.CDS1 32068608 32069168
chr_1 g13723 g13723.t12 TTS g13723.t12 32069665 32069665

Sequences

>g13723.t12 Gene=g13723 Length=1196
AAAAGTCGTTTAGTTAAAGTGTACAGATCGTTTCTGGTGGCTTCAGTTTCTTGTAGTGAA
GGTTCAAATGTGTGATGATGATGTTGCTGCATTGGTCGTTGACAATGGCTCAGGAATGTG
CAAAGCTGGCTTCGCTGGTGATGACGCTCCACGTGCTGTCTTCCCATCAATCGTAGGTCG
CCCACGTCATCAAGGTGTTATGGTCGGTATGGGTCAAAAGGACTCATATGTTGGTGATGA
GGCCCAAAGCAAAGAGGTATCCTTACCTTGAAATACCCAATTGAGCACGGTATCATCACA
AACTGGGATGATATGGAGAAGATCTGGCATCACACTTTCTACAATGAACTTCGCGTTGCC
CCAGAAGAGCACCCAGTCTTGCTCACAGAAGCTCCATTGAACCCAAAGGCTAACCGCGAG
AAGATGACACAAATCATGTTTGAAACATTCAACTCACCAGCTATGTATGTTGCCATCCAA
GCCGTTCTCTCATTGTACGCCTCAGGTCGTACCACCGGTATTGTTTTGGATTCAGGAGAT
GTGTCTCACACACAGTCCCAATTTATGAAGGTTATGCTTTGCCACATGCCATCCTCCGTC
TTGACTTGGCCGGTCGCGACTTGACTGACTACTTGATGAAGATCTTGACCGAACGCGGTT
ACTCATTCGTCACAACAGCTGAACGTGAAATCGTTCGTGACATCAAGGAAAAGTTGTGCT
ATGTTGCATTGGACTTCGAACAAGAAATGGCCACCGCTGCTGCCTCAACCTCACTCGAGA
AGTCATATGAATTGCCTGATGGTCAAGTTATCACCATCGGTAACGAACGTTTCCGTTGCC
CAGAATCATTGTTCCAACCATCATTCTTGGGTATGGAATCATGCGGTATTCACGAAACCG
TCTACAATTCAATCATGAAGTGCGATGTTGATATCCGTAAGGACTTGTACGCCAACAACG
TCTTATCAGGTGGCACAACAATGTACCCAGGTATTGCCGATCGTATGCAAAAGGAAATGA
CTGCCCTCGCTCCATCAACAATCAAGATCAAGATCATTGCTCCACCAGAACGTAAATACT
CAGTCTGGATCGGAGGTTCAATCTTGGCATCACTCTCAACCTTCCAGCAGATGTGGATCT
CAAAGGAAGAATACGACGAATCAGGCCCAGGCATTGTTCACCGCAAGTGCTTCTAA

>g13723.t12 Gene=g13723 Length=186
MKILTERGYSFVTTAEREIVRDIKEKLCYVALDFEQEMATAAASTSLEKSYELPDGQVIT
IGNERFRCPESLFQPSFLGMESCGIHETVYNSIMKCDVDIRKDLYANNVLSGGTTMYPGI
ADRMQKEMTALAPSTIKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKEEYDESGPGI
VHRKCF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g13723.t12 Gene3D G3DSA:3.90.640.10 Actin; Chain A 1 85 6.4E-88
9 g13723.t12 Gene3D G3DSA:3.30.420.40 - 86 148 6.4E-88
8 g13723.t12 Gene3D G3DSA:3.30.420.40 - 149 182 6.4E-88
2 g13723.t12 PANTHER PTHR11937:SF397 ACTIN, INDIRECT FLIGHT MUSCLE-RELATED 1 185 2.0E-118
3 g13723.t12 PANTHER PTHR11937 ACTIN 1 185 2.0E-118
1 g13723.t12 Pfam PF00022 Actin 6 186 5.1E-69
6 g13723.t12 ProSitePatterns PS00432 Actins signature 2. 167 175 -
5 g13723.t12 SMART SM00268 actin_3 1 186 1.7E-22
4 g13723.t12 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