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.t52 TTS g11466.t52 16397069 16397069
chr_1 g11466 g11466.t52 isoform g11466.t52 16397451 16407074
chr_1 g11466 g11466.t52 exon g11466.t52.exon1 16397451 16397553
chr_1 g11466 g11466.t52 cds g11466.t52.CDS1 16397550 16397553
chr_1 g11466 g11466.t52 exon g11466.t52.exon2 16399500 16399573
chr_1 g11466 g11466.t52 cds g11466.t52.CDS2 16399500 16399573
chr_1 g11466 g11466.t52 exon g11466.t52.exon3 16400629 16400691
chr_1 g11466 g11466.t52 cds g11466.t52.CDS3 16400629 16400691
chr_1 g11466 g11466.t52 exon g11466.t52.exon4 16400819 16400894
chr_1 g11466 g11466.t52 cds g11466.t52.CDS4 16400819 16400894
chr_1 g11466 g11466.t52 exon g11466.t52.exon5 16401901 16401971
chr_1 g11466 g11466.t52 cds g11466.t52.CDS5 16401901 16401971
chr_1 g11466 g11466.t52 exon g11466.t52.exon6 16402845 16402962
chr_1 g11466 g11466.t52 cds g11466.t52.CDS6 16402845 16402962
chr_1 g11466 g11466.t52 exon g11466.t52.exon7 16403395 16403528
chr_1 g11466 g11466.t52 cds g11466.t52.CDS7 16403395 16403528
chr_1 g11466 g11466.t52 exon g11466.t52.exon8 16406585 16406868
chr_1 g11466 g11466.t52 cds g11466.t52.CDS8 16406585 16406824
chr_1 g11466 g11466.t52 exon g11466.t52.exon9 16407017 16407074
chr_1 g11466 g11466.t52 TSS g11466.t52 16407060 16407060

Sequences

>g11466.t52 Gene=g11466 Length=981
TAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGTTC
TCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGAAA
AAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTGAA
CAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACATTG
CAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTCTT
GTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCGCT
GCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTTTG
GCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGTGCC
CGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTTGAAAAT
CAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAGGTTGCA
CGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTGCAGAAGCTGGT
GAAGCCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAAGTCA
TTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGAAGAATATAAGAATCAAATTAAG
ACTCTTACCACCCGCCTTAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTT
CAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGGTACATGAGCTTGTTTCCGAAAAGGA
GAAATACAGAGAAATTGGAGACGATCTCGATACCGCTTTTGTGGAACTCATCCTTAAGGA
ATAAAGGATTTTCGGCCTACA

>g11466.t52 Gene=g11466 Length=259
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEAKIVELEEELRVVGNNLKSLEVSEEKANQREEEYKNQIKTLTTRLKEAEARAE
FAERSVQKLQKEVDRLEGT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g11466.t52 Coils Coil Coil 1 259 -
11 g11466.t52 Gene3D G3DSA:1.20.5.340 - 1 96 7.4E-36
12 g11466.t52 Gene3D G3DSA:1.20.5.340 - 97 140 1.6E-5
10 g11466.t52 Gene3D G3DSA:1.20.5.340 - 159 258 3.4E-22
2 g11466.t52 PANTHER PTHR19269 TROPOMYOSIN 1 258 5.7E-109
5 g11466.t52 PRINTS PR00194 Tropomyosin signature 84 101 2.8E-59
7 g11466.t52 PRINTS PR00194 Tropomyosin signature 120 140 2.8E-59
3 g11466.t52 PRINTS PR00194 Tropomyosin signature 145 173 2.8E-59
6 g11466.t52 PRINTS PR00194 Tropomyosin signature 175 198 2.8E-59
4 g11466.t52 PRINTS PR00194 Tropomyosin signature 231 256 2.8E-59
1 g11466.t52 Pfam PF00261 Tropomyosin 48 257 2.0E-84
9 g11466.t52 ProSitePatterns PS00326 Tropomyosins signature. 232 240 -
8 g11466.t52 SUPERFAMILY SSF57997 Tropomyosin 1 258 3.05E-87

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

Pathway

  • This transcript belongs to the following pathways

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