Gene loci information

Transcript annotation

  • This transcript has been annotated as Tropomyosin-2.

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.t70 isoform g11466.t70 16400653 16407076
chr_1 g11466 g11466.t70 exon g11466.t70.exon1 16400653 16400691
chr_1 g11466 g11466.t70 cds g11466.t70.CDS1 16400653 16400691
chr_1 g11466 g11466.t70 exon g11466.t70.exon2 16400819 16400894
chr_1 g11466 g11466.t70 cds g11466.t70.CDS2 16400819 16400894
chr_1 g11466 g11466.t70 exon g11466.t70.exon3 16401559 16401629
chr_1 g11466 g11466.t70 cds g11466.t70.CDS3 16401559 16401629
chr_1 g11466 g11466.t70 exon g11466.t70.exon4 16403142 16403259
chr_1 g11466 g11466.t70 cds g11466.t70.CDS4 16403142 16403259
chr_1 g11466 g11466.t70 exon g11466.t70.exon5 16403395 16403528
chr_1 g11466 g11466.t70 cds g11466.t70.CDS5 16403395 16403528
chr_1 g11466 g11466.t70 exon g11466.t70.exon6 16406585 16406868
chr_1 g11466 g11466.t70 cds g11466.t70.CDS6 16406585 16406824
chr_1 g11466 g11466.t70 exon g11466.t70.exon7 16407017 16407076
chr_1 g11466 g11466.t70 TSS g11466.t70 16407060 16407060
chr_1 g11466 g11466.t70 TTS g11466.t70 NA NA

Sequences

>g11466.t70 Gene=g11466 Length=782
AGTAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGT
TCTCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGA
AAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTG
AACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACAT
TGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTC
TTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCG
CTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTT
TGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGAA
TAAGAAAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCTAGAAG
CTCAATTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGAGGTCG
CCAGAAAATTAGTTTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGAATTAA
GCGAAAGCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAAGT
CATTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGAAGAATATAAGAATCAAATTA
AG

>g11466.t70 Gene=g11466 Length=226
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERIRKALENRTNMEDDRVAILEAQLTQAKLIAEEADKKYEEVARKLVLMEQDLERSE
EKVELSESKIVELEEELRVVGNNLKSLEVSEEKANQREEEYKNQIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11466.t70 Coils Coil Coil 1 139 -
11 g11466.t70 Coils Coil Coil 141 226 -
8 g11466.t70 Gene3D G3DSA:1.20.5.340 - 1 94 5.0E-36
9 g11466.t70 Gene3D G3DSA:1.20.5.340 - 95 139 2.1E-7
10 g11466.t70 Gene3D G3DSA:1.20.5.340 - 159 226 7.9E-8
2 g11466.t70 PANTHER PTHR19269 TROPOMYOSIN 1 226 2.4E-79
4 g11466.t70 PRINTS PR00194 Tropomyosin signature 84 101 9.6E-40
6 g11466.t70 PRINTS PR00194 Tropomyosin signature 120 140 9.6E-40
3 g11466.t70 PRINTS PR00194 Tropomyosin signature 145 173 9.6E-40
5 g11466.t70 PRINTS PR00194 Tropomyosin signature 175 198 9.6E-40
1 g11466.t70 Pfam PF00261 Tropomyosin 48 226 1.1E-66
7 g11466.t70 SUPERFAMILY SSF57997 Tropomyosin 1 226 1.44E-69

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.

Raw TPM values