Gene loci information

Transcript annotation

  • This transcript has been annotated as Tropomyosin-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_1 g11464 g11464.t33 isoform g11464.t33 16393339 16395040
chr_1 g11464 g11464.t33 exon g11464.t33.exon1 16393339 16393369
chr_1 g11464 g11464.t33 cds g11464.t33.CDS1 16393340 16393369
chr_1 g11464 g11464.t33 exon g11464.t33.exon2 16393544 16393763
chr_1 g11464 g11464.t33 cds g11464.t33.CDS2 16393544 16393763
chr_1 g11464 g11464.t33 exon g11464.t33.exon3 16393833 16394255
chr_1 g11464 g11464.t33 cds g11464.t33.CDS3 16393833 16394206
chr_1 g11464 g11464.t33 exon g11464.t33.exon4 16395006 16395040
chr_1 g11464 g11464.t33 TSS g11464.t33 16395053 16395053
chr_1 g11464 g11464.t33 TTS g11464.t33 NA NA

Sequences

>g11464.t33 Gene=g11464 Length=709
ATTTTGTGTTGCGAGGATCTTTATAGAGCGCTCAGTTATTTTCATTAGCATTATTTTCGA
GTAGAACAAAGAAAAAGCCTAAAAATGGACGCCATTAAGAAGAAGATGCAAGCAATGAAG
CTTGAGAAAGATAATGCTCAAGACAAAGCTGACACCTGCGAGAATCAAGCCAAGGATGCC
AACGCCAAGGCCGCTAAGGTCGAAGAAGAAGTTGCCGATTTGATCAAGAAATTGGCTCAA
GTTGAAAGCGATTTGGAAGCACACAAGAATGCTTTGGAGCAAGCCAACAAGGATTTAGAA
GAAAAAGAAAAGCTCCTCACAACCACAGAATCAGAAGTTGCTGCATTAAACAGAAAAGTA
CAACAGGTTGAAGAAGATTTGGAAAAGTCAGAAGAACGCTCATCAACTGCTATGCAAAAA
CTTTTGGAAGCCACACAAGCTGCTGATGAAAATAACCGTATGTGCAAGGTATTGGAGAAT
CGTGCACAGCAAGATGAAGAGCGCATGGATCAATTGACAAACCAACTTAAAGAAGCACGT
CTCCTTGCTGAAGACGCCGATGGTAAATCAGATGAAGTTTCACGCAAGTTGGCCTTCGTT
GAAGATGAATTGGAAGTTGCTGAAGATCGTGTTAAGTCAGGAGAGGCAAAGATCATGGAA
CTTGAAGAAGAATTGAAGGTTGTTGGTAACTCATTGAAATCATTGGAAG

>g11464.t33 Gene=g11464 Length=208
MDAIKKKMQAMKLEKDNAQDKADTCENQAKDANAKAAKVEEEVADLIKKLAQVESDLEAH
KNALEQANKDLEEKEKLLTTTESEVAALNRKVQQVEEDLEKSEERSSTAMQKLLEATQAA
DENNRMCKVLENRAQQDEERMDQLTNQLKEARLLAEDADGKSDEVSRKLAFVEDELEVAE
DRVKSGEAKIMELEEELKVVGNSLKSLE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11464.t33 Coils Coil Coil 1 112 -
13 g11464.t33 Coils Coil Coil 120 208 -
12 g11464.t33 Gene3D G3DSA:1.20.5.340 - 1 79 2.2E-24
11 g11464.t33 Gene3D G3DSA:1.20.5.340 - 80 140 7.5E-9
10 g11464.t33 Gene3D G3DSA:1.20.5.340 - 159 208 5.1E-6
9 g11464.t33 MobiDBLite mobidb-lite consensus disorder prediction 1 27 -
2 g11464.t33 PANTHER PTHR19269:SF53 TROPOMYOSIN-2 1 208 1.6E-111
3 g11464.t33 PANTHER PTHR19269 TROPOMYOSIN 1 208 1.6E-111
5 g11464.t33 PRINTS PR00194 Tropomyosin signature 84 101 1.0E-33
7 g11464.t33 PRINTS PR00194 Tropomyosin signature 120 140 1.0E-33
4 g11464.t33 PRINTS PR00194 Tropomyosin signature 145 173 1.0E-33
6 g11464.t33 PRINTS PR00194 Tropomyosin signature 175 198 1.0E-33
1 g11464.t33 Pfam PF00261 Tropomyosin 48 208 6.3E-49
8 g11464.t33 SUPERFAMILY SSF57997 Tropomyosin 1 208 2.29E-61

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