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.t31 isoform g11466.t31 16397067 16407076
chr_1 g11466 g11466.t31 exon g11466.t31.exon1 16397067 16397553
chr_1 g11466 g11466.t31 TTS g11466.t31 16397069 16397069
chr_1 g11466 g11466.t31 cds g11466.t31.CDS1 16397468 16397553
chr_1 g11466 g11466.t31 exon g11466.t31.exon2 16399504 16399573
chr_1 g11466 g11466.t31 cds g11466.t31.CDS2 16399504 16399573
chr_1 g11466 g11466.t31 exon g11466.t31.exon3 16400629 16400691
chr_1 g11466 g11466.t31 cds g11466.t31.CDS3 16400629 16400691
chr_1 g11466 g11466.t31 exon g11466.t31.exon4 16400819 16400894
chr_1 g11466 g11466.t31 cds g11466.t31.CDS4 16400819 16400894
chr_1 g11466 g11466.t31 exon g11466.t31.exon5 16401901 16401971
chr_1 g11466 g11466.t31 cds g11466.t31.CDS5 16401901 16401971
chr_1 g11466 g11466.t31 exon g11466.t31.exon6 16402845 16402962
chr_1 g11466 g11466.t31 cds g11466.t31.CDS6 16402845 16402916
chr_1 g11466 g11466.t31 exon g11466.t31.exon7 16403391 16403528
chr_1 g11466 g11466.t31 exon g11466.t31.exon8 16406585 16406868
chr_1 g11466 g11466.t31 exon g11466.t31.exon9 16407017 16407076
chr_1 g11466 g11466.t31 TSS g11466.t31 16407060 16407060

Sequences

>g11466.t31 Gene=g11466 Length=1367
AGTAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGT
TCTCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGA
AAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTG
AACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACAT
TGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTC
TTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCG
CTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTT
TGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGGT
AATGCCCGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTT
GAAAATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAG
GTTGCACGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTGCAGAA
GCTGGTGAAGCCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTG
AAGTCATTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGAAGAATATAAGAATCAA
ATTAAGACTCTTACCACCCGCCTTAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACGT
TCAGTTCAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGATGAGCTTGTTTCCGAAAAG
GAGAAATACAGAGAAATTGGAGACGATCTCGATACCGCTTTTGTGGAACTCATCCTTAAG
GAATAAAGGATTTTCGGCCTACAAAAACATCAAAGCTTACAATGAAATGAACGTTTTACA
TAAATTTGAAAAACTCTTACTCTTCAAAATCTTTTTTCTAATTTATTAATTTTCCTTCAG
TTAACGCGCATCGATATACATATATTGTGGATAAGATCAAAGATAGAATTAGGAAAAATT
TATTCATATTAAGCATGTAAAGTTTATCATTTAAATATTACAACCAAGATCATAAGAGAT
ATAGAGATAAATGTAAAACTGCAAATAACATCAATCTGAAATCTCTCACTCTTGATCGAA
ATTGGGGTTTAGGAATAAAGTTAAAACGCCAACATCAGCGAACAAAATTTTTGATATATT
TTTTAATTTCAAAATGCAAAAATAAAAAGTTTCTTTTTAGAATGTTT

>g11466.t31 Gene=g11466 Length=145
MDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAEERAEAGEAKIVELEEELRVV
GNNLKSLEVSEEKANQREEEYKNQIKTLTTRLKEAEARAEFAERSVQKLQKEVDRLEDEL
VSEKEKYREIGDDLDTAFVELILKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11466.t31 Coils Coil Coil 1 133 -
9 g11466.t31 Gene3D G3DSA:1.20.5.340 - 19 119 1.7E-23
2 g11466.t31 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 1 142 4.1E-71
3 g11466.t31 PANTHER PTHR19269 TROPOMYOSIN 1 142 4.1E-71
6 g11466.t31 PRINTS PR00194 Tropomyosin signature 5 33 1.4E-38
5 g11466.t31 PRINTS PR00194 Tropomyosin signature 35 58 1.4E-38
4 g11466.t31 PRINTS PR00194 Tropomyosin signature 91 116 1.4E-38
1 g11466.t31 Pfam PF00261 Tropomyosin 1 142 8.0E-60
8 g11466.t31 ProSitePatterns PS00326 Tropomyosins signature. 92 100 -
7 g11466.t31 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