Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Tropomyosin-1, isoforms 9A/A/B.

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.t57 TTS g11466.t57 16398326 16398326
chr_1 g11466 g11466.t57 isoform g11466.t57 16399209 16404362
chr_1 g11466 g11466.t57 exon g11466.t57.exon1 16399209 16399291
chr_1 g11466 g11466.t57 exon g11466.t57.exon2 16399500 16399573
chr_1 g11466 g11466.t57 exon g11466.t57.exon3 16400314 16400376
chr_1 g11466 g11466.t57 exon g11466.t57.exon4 16400819 16400894
chr_1 g11466 g11466.t57 exon g11466.t57.exon5 16401559 16401621
chr_1 g11466 g11466.t57 cds g11466.t57.CDS1 16401571 16401621
chr_1 g11466 g11466.t57 exon g11466.t57.exon6 16403142 16403259
chr_1 g11466 g11466.t57 cds g11466.t57.CDS2 16403142 16403259
chr_1 g11466 g11466.t57 exon g11466.t57.exon7 16403395 16403528
chr_1 g11466 g11466.t57 cds g11466.t57.CDS3 16403395 16403528
chr_1 g11466 g11466.t57 exon g11466.t57.exon8 16404204 16404362
chr_1 g11466 g11466.t57 cds g11466.t57.CDS4 16404204 16404347
chr_1 g11466 g11466.t57 TSS g11466.t57 16404668 16404668

Sequences

>g11466.t57 Gene=g11466 Length=770
AAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGATGTTCTCAAG
AAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATGTGAAGAATTT
AATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGAAGTCGCTGCT
TTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCA
TCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGAATAAGA
AAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCTAGAAGCTCAA
TTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGAGAAAATTAGT
TTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGAATTAAGCGAAAGCAAAAT
TGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAAGTCATTGGAAGTGTC
AGAAGAGAAGGCAACACAAAGGGAGGAGACGTTTGAAGGTCAAGTGAGAATACTGGAAGG
ACACTTAAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTTCAGAAATTGCA
GAAAGAAGTCGACAGACTTGAAGGTACATGAATTGTTAAATGAGCGTGCACGAAACAAGA
TGCTCCAGGAAGAAATGGAAGCGACACTTCATGATATTCAGAATATGTAA

>g11466.t57 Gene=g11466 Length=148
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEKISFDGARFRAFRRKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11466.t57 Coils Coil Coil 11 107 -
10 g11466.t57 Coils Coil Coil 109 129 -
8 g11466.t57 Gene3D G3DSA:1.20.5.340 - 8 107 4.0E-15
2 g11466.t57 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 12 132 1.6E-37
3 g11466.t57 PANTHER PTHR19269 TROPOMYOSIN 12 132 1.6E-37
5 g11466.t57 PRINTS PR00194 Tropomyosin signature 52 69 2.3E-19
4 g11466.t57 PRINTS PR00194 Tropomyosin signature 88 108 2.3E-19
6 g11466.t57 PRINTS PR00194 Tropomyosin signature 113 141 2.3E-19
1 g11466.t57 Pfam PF00261 Tropomyosin 16 132 1.3E-37
7 g11466.t57 SUPERFAMILY SSF57997 Tropomyosin 11 133 4.41E-29

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