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.t67 isoform g11466.t67 16400653 16406824
chr_1 g11466 g11466.t67 exon g11466.t67.exon1 16400653 16400691
chr_1 g11466 g11466.t67 cds g11466.t67.CDS1 16400653 16400691
chr_1 g11466 g11466.t67 exon g11466.t67.exon2 16400819 16400894
chr_1 g11466 g11466.t67 cds g11466.t67.CDS2 16400819 16400894
chr_1 g11466 g11466.t67 exon g11466.t67.exon3 16401901 16401971
chr_1 g11466 g11466.t67 cds g11466.t67.CDS3 16401901 16401971
chr_1 g11466 g11466.t67 exon g11466.t67.exon4 16402845 16402962
chr_1 g11466 g11466.t67 cds g11466.t67.CDS4 16402845 16402962
chr_1 g11466 g11466.t67 exon g11466.t67.exon5 16403395 16403528
chr_1 g11466 g11466.t67 cds g11466.t67.CDS5 16403395 16403528
chr_1 g11466 g11466.t67 exon g11466.t67.exon6 16406585 16406824
chr_1 g11466 g11466.t67 cds g11466.t67.CDS6 16406585 16406824
chr_1 g11466 g11466.t67 TSS g11466.t67 16407060 16407060
chr_1 g11466 g11466.t67 TTS g11466.t67 NA NA

Sequences

>g11466.t67 Gene=g11466 Length=678
ATGGATGCGATTAAGAAAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGAT
CGCGCCCTTCTCTGTGAACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAA
GAAGAGGCCCGCACATTGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACA
CAAGAACAAGAGACTCTTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAAT
GCTGAATCAGAAGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAA
CGTTCTGAAGAGCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCT
GATGAATCTGAACGTGCCCGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGT
ATGGATGCTCTTGAAAATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAG
AAATACGATGAGGTTGCACGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAA
GAGCGTGCAGAAGCTGGTGAAGCCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTC
GGTAACAACTTGAAGTCATTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGAAGAA
TATAAGAATCAAATTAAG

>g11466.t67 Gene=g11466 Length=226
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEAKIVELEEELRVVGNNLKSLEVSEEKANQREEEYKNQIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11466.t67 Coils Coil Coil 1 226 -
9 g11466.t67 Gene3D G3DSA:1.20.5.340 - 1 96 5.3E-36
8 g11466.t67 Gene3D G3DSA:1.20.5.340 - 97 139 1.1E-5
10 g11466.t67 Gene3D G3DSA:1.20.5.340 - 159 226 3.0E-10
2 g11466.t67 PANTHER PTHR19269 TROPOMYOSIN 1 226 4.4E-90
4 g11466.t67 PRINTS PR00194 Tropomyosin signature 84 101 2.1E-44
6 g11466.t67 PRINTS PR00194 Tropomyosin signature 120 140 2.1E-44
3 g11466.t67 PRINTS PR00194 Tropomyosin signature 145 173 2.1E-44
5 g11466.t67 PRINTS PR00194 Tropomyosin signature 175 198 2.1E-44
1 g11466.t67 Pfam PF00261 Tropomyosin 48 226 6.8E-69
7 g11466.t67 SUPERFAMILY SSF57997 Tropomyosin 1 226 1.06E-74

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