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.t24 isoform g11466.t24 16397067 16407046
chr_1 g11466 g11466.t24 exon g11466.t24.exon1 16397067 16397553
chr_1 g11466 g11466.t24 TTS g11466.t24 16397069 16397069
chr_1 g11466 g11466.t24 exon g11466.t24.exon2 16399504 16399573
chr_1 g11466 g11466.t24 exon g11466.t24.exon3 16400629 16400691
chr_1 g11466 g11466.t24 exon g11466.t24.exon4 16401880 16401971
chr_1 g11466 g11466.t24 cds g11466.t24.CDS1 16401897 16401971
chr_1 g11466 g11466.t24 exon g11466.t24.exon5 16402845 16402962
chr_1 g11466 g11466.t24 cds g11466.t24.CDS2 16402845 16402962
chr_1 g11466 g11466.t24 exon g11466.t24.exon6 16403395 16403528
chr_1 g11466 g11466.t24 cds g11466.t24.CDS3 16403395 16403528
chr_1 g11466 g11466.t24 exon g11466.t24.exon7 16406585 16406868
chr_1 g11466 g11466.t24 cds g11466.t24.CDS4 16406585 16406824
chr_1 g11466 g11466.t24 exon g11466.t24.exon8 16407017 16407046
chr_1 g11466 g11466.t24 TSS g11466.t24 16407060 16407060

Sequences

>g11466.t24 Gene=g11466 Length=1278
ACTGTTCAAGTCGCGGATTCAGATTCAAGTTCTCTGGTGCTTTCGTAATACCGTAGTAAA
AACACATTACCAAAATGGATGCGATTAAGAAAAAAATGCAAGCAATGAAGCTTGAGAAGG
ATAACGCATTAGATCGCGCCCTTCTCTGTGAACAGCAAGCTCGTGATGCAAACACACGTG
CTGAAAAGGCCGAAGAAGAGGCCCGCACATTGCAAAAGAAGATCCAAACAATTGAAAATG
ATTTGGATCAGACACAAGAACAAGAGACTCTTGTTAATGGAAAGCTTGAAGAAAAAGAAA
AGGCACTTCAAAATGCTGAATCAGAAGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGG
AAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAG
CATCAGCTGCTGCTGATGAATCTGAACGTGCCCGTAAAGTTCTTGAAAACCGTTCACTTG
CCGATGAAGAGCGTATGGATGCTCTTGAAAATCAATTGAAGGAAGCTCGCTTCCTCGCTG
AAGAAGCTGACAAGAAATACGATGAGGTTGCACGTAAATTAGCTATGGTTGAGGCTGATC
TTGAACGTGCAGAAGAGCGTGCAGAAGCTGGTGAAGCGTAAGAGTCTTCATGAATTGTGC
AAATCAACGTGAAGAAGAATATAAGAATCAAATTAAGACTCTTACCACCCGCCTTAAGGA
GGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTTCAGAAATTGCAGAAAGAAGTCGA
CAGACTTGAAGATGAGCTTGTTTCCGAAAAGGAGAAATACAGAGAAATTGGAGACGATCT
CGATACCGCTTTTGTGGAACTCATCCTTAAGGAATAAAGGATTTTCGGCCTACAAAAACA
TCAAAGCTTACAATGAAATGAACGTTTTACATAAATTTGAAAAACTCTTACTCTTCAAAA
TCTTTTTTCTAATTTATTAATTTTCCTTCAGTTAACGCGCATCGATATACATATATTGTG
GATAAGATCAAAGATAGAATTAGGAAAAATTTATTCATATTAAGCATGTAAAGTTTATCA
TTTAAATATTACAACCAAGATCATAAGAGATATAGAGATAAATGTAAAACTGCAAATAAC
ATCAATCTGAAATCTCTCACTCTTGATCGAAATTGGGGTTTAGGAATAAAGTTAAAACGC
CAACATCAGCGAACAAAATTTTTGATATATTTTTTAATTTCAAAATGCAAAAATAAAAAG
TTTCTTTTTAGAATGTTT

>g11466.t24 Gene=g11466 Length=188
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11466.t24 Coils Coil Coil 1 182 -
11 g11466.t24 Gene3D G3DSA:1.20.5.340 - 1 96 3.2E-36
10 g11466.t24 Gene3D G3DSA:1.20.5.340 - 97 139 1.4E-5
8 g11466.t24 MobiDBLite mobidb-lite consensus disorder prediction 106 136 -
9 g11466.t24 MobiDBLite mobidb-lite consensus disorder prediction 118 136 -
2 g11466.t24 PANTHER PTHR19269 TROPOMYOSIN 1 188 6.6E-68
4 g11466.t24 PRINTS PR00194 Tropomyosin signature 84 101 7.7E-39
5 g11466.t24 PRINTS PR00194 Tropomyosin signature 120 140 7.7E-39
3 g11466.t24 PRINTS PR00194 Tropomyosin signature 145 173 7.7E-39
6 g11466.t24 PRINTS PR00194 Tropomyosin signature 175 188 7.7E-39
1 g11466.t24 Pfam PF00261 Tropomyosin 48 187 4.7E-50
7 g11466.t24 SUPERFAMILY SSF57997 Tropomyosin 1 187 1.47E-60

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