Gene loci information

Transcript annotation

  • This transcript has been annotated as Tropomyosin.

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 g11466 g11466.t13 isoform g11466.t13 16397067 16402920
chr_1 g11466 g11466.t13 exon g11466.t13.exon1 16397067 16397553
chr_1 g11466 g11466.t13 TTS g11466.t13 16397069 16397069
chr_1 g11466 g11466.t13 cds g11466.t13.CDS1 16397468 16397553
chr_1 g11466 g11466.t13 exon g11466.t13.exon2 16399504 16399573
chr_1 g11466 g11466.t13 cds g11466.t13.CDS2 16399504 16399573
chr_1 g11466 g11466.t13 exon g11466.t13.exon3 16400629 16400691
chr_1 g11466 g11466.t13 cds g11466.t13.CDS3 16400629 16400691
chr_1 g11466 g11466.t13 exon g11466.t13.exon4 16400819 16400894
chr_1 g11466 g11466.t13 cds g11466.t13.CDS4 16400819 16400894
chr_1 g11466 g11466.t13 exon g11466.t13.exon5 16401901 16401971
chr_1 g11466 g11466.t13 cds g11466.t13.CDS5 16401901 16401971
chr_1 g11466 g11466.t13 exon g11466.t13.exon6 16402845 16402920
chr_1 g11466 g11466.t13 cds g11466.t13.CDS6 16402845 16402916
chr_1 g11466 g11466.t13 TSS g11466.t13 NA NA

Sequences

>g11466.t13 Gene=g11466 Length=843
GCGTATGGATGCTCTTGAAAATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGA
CAAGAAATACGATGAGGTTGCACGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGC
AGAAGAGCGTGCAGAAGCTGGTGAAGCCAAAATTGTTGAACTTGAAGAAGAACTTCGCGT
CGTCGGTAACAACTTGAAGTCATTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGA
AGAATATAAGAATCAAATTAAGACTCTTACCACCCGCCTTAAGGAGGCTGAAGCCAGAGC
CGAATTTGCTGAACGTTCAGTTCAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGATGA
GCTTGTTTCCGAAAAGGAGAAATACAGAGAAATTGGAGACGATCTCGATACCGCTTTTGT
GGAACTCATCCTTAAGGAATAAAGGATTTTCGGCCTACAAAAACATCAAAGCTTACAATG
AAATGAACGTTTTACATAAATTTGAAAAACTCTTACTCTTCAAAATCTTTTTTCTAATTT
ATTAATTTTCCTTCAGTTAACGCGCATCGATATACATATATTGTGGATAAGATCAAAGAT
AGAATTAGGAAAAATTTATTCATATTAAGCATGTAAAGTTTATCATTTAAATATTACAAC
CAAGATCATAAGAGATATAGAGATAAATGTAAAACTGCAAATAACATCAATCTGAAATCT
CTCACTCTTGATCGAAATTGGGGTTTAGGAATAAAGTTAAAACGCCAACATCAGCGAACA
AAATTTTTGATATATTTTTTAATTTCAAAATGCAAAAATAAAAAGTTTCTTTTTAGAATG
TTT

>g11466.t13 Gene=g11466 Length=145
MDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAEERAEAGEAKIVELEEELRVV
GNNLKSLEVSEEKANQREEEYKNQIKTLTTRLKEAEARAEFAERSVQKLQKEVDRLEDEL
VSEKEKYREIGDDLDTAFVELILKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11466.t13 Coils Coil Coil 1 133 -
9 g11466.t13 Gene3D G3DSA:1.20.5.340 - 19 119 1.7E-23
2 g11466.t13 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 1 142 4.1E-71
3 g11466.t13 PANTHER PTHR19269 TROPOMYOSIN 1 142 4.1E-71
6 g11466.t13 PRINTS PR00194 Tropomyosin signature 5 33 1.4E-38
5 g11466.t13 PRINTS PR00194 Tropomyosin signature 35 58 1.4E-38
4 g11466.t13 PRINTS PR00194 Tropomyosin signature 91 116 1.4E-38
1 g11466.t13 Pfam PF00261 Tropomyosin 1 142 8.0E-60
8 g11466.t13 ProSitePatterns PS00326 Tropomyosins signature. 92 100 -
7 g11466.t13 SUPERFAMILY SSF57997 Tropomyosin 1 141 7.85E-48

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