Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t4 isoform g11466.t4 16396537 16404362
chr_1 g11466 g11466.t4 exon g11466.t4.exon1 16396537 16396907
chr_1 g11466 g11466.t4 cds g11466.t4.CDS1 16396856 16396907
chr_1 g11466 g11466.t4 exon g11466.t4.exon2 16399500 16399573
chr_1 g11466 g11466.t4 cds g11466.t4.CDS2 16399500 16399573
chr_1 g11466 g11466.t4 exon g11466.t4.exon3 16399948 16400010
chr_1 g11466 g11466.t4 cds g11466.t4.CDS3 16399948 16400010
chr_1 g11466 g11466.t4 exon g11466.t4.exon4 16400819 16400894
chr_1 g11466 g11466.t4 cds g11466.t4.CDS4 16400819 16400894
chr_1 g11466 g11466.t4 exon g11466.t4.exon5 16401559 16401629
chr_1 g11466 g11466.t4 cds g11466.t4.CDS5 16401559 16401629
chr_1 g11466 g11466.t4 exon g11466.t4.exon6 16403142 16403259
chr_1 g11466 g11466.t4 cds g11466.t4.CDS6 16403142 16403259
chr_1 g11466 g11466.t4 exon g11466.t4.exon7 16403395 16403528
chr_1 g11466 g11466.t4 cds g11466.t4.CDS7 16403395 16403528
chr_1 g11466 g11466.t4 exon g11466.t4.exon8 16404204 16404362
chr_1 g11466 g11466.t4 cds g11466.t4.CDS8 16404204 16404347
chr_1 g11466 g11466.t4 TSS g11466.t4 16404668 16404668
chr_1 g11466 g11466.t4 TTS g11466.t4 NA NA

Sequences

>g11466.t4 Gene=g11466 Length=1066
AAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGATGTTCTCAAG
AAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATGTGAAGAATTT
AATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGAAGTCGCTGCT
TTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCA
TCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGAATAAGA
AAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCTAGAAGCTCAA
TTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGAGGTCGCCAGA
AAATTAGTTTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGAATTAAGCGAA
AGCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAAGTCATTG
GAAGTGTCAGAAGAGAAGGCAAATGCAACCAATGAAACAGTCGAGGCGAAAGTTCATCAA
TTGAATGAAAAATTAACCACTGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTTCAG
AAATTGCAGAAAGAAGTCGACAGACTTGAAGGTACAAGAATTGGTACAGGAAAGGTCAAA
GTTCAAAGCAGTAGCAAATCAACTTGATCTCACTTATCATGAACTTCATGGATGCTAAAG
GTTAAAGACAAATCAAAAGGAAAATCACTCGCCTCGAGCATGCTAAATATTTTTTATATT
TTTCGTTTCACTCTACATTCCCAAAAAGAAGATAATGCATTTAAAGCAGTTTGTACTTCA
TTTTTTTCTTGCTTATAATTATCATTTAAAACATTCAAATTTTGAAATATAAAAATATTA
AGAAAGTAATTCAATGTTTTTACTTTGATTTAAGATCAAATTGCTTAAAACCGTATTAAA
AGTGCTTAAAAATAAAAAAATTTCAATTGATGAATGCTAAAAAAAA

>g11466.t4 Gene=g11466 Length=243
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEVARKLVLMEQDLERSEEKVELSESKIVELEEELRVVGNNLKSLEVSEE
KANATNETVEAKVHQLNEKLTTAEARAEFAERSVQKLQKEVDRLEGTRIGTGKVKVQSSS
KST

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11466.t4 Coils Coil Coil 11 107 -
13 g11466.t4 Coils Coil Coil 109 227 -
11 g11466.t4 Gene3D G3DSA:1.20.5.340 - 8 107 1.4E-14
10 g11466.t4 Gene3D G3DSA:1.20.5.340 - 127 226 4.8E-17
2 g11466.t4 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 12 228 2.8E-80
3 g11466.t4 PANTHER PTHR19269 TROPOMYOSIN 12 228 2.8E-80
7 g11466.t4 PRINTS PR00194 Tropomyosin signature 52 69 5.8E-53
5 g11466.t4 PRINTS PR00194 Tropomyosin signature 88 108 5.8E-53
8 g11466.t4 PRINTS PR00194 Tropomyosin signature 113 141 5.8E-53
6 g11466.t4 PRINTS PR00194 Tropomyosin signature 143 166 5.8E-53
4 g11466.t4 PRINTS PR00194 Tropomyosin signature 199 224 5.8E-53
1 g11466.t4 Pfam PF00261 Tropomyosin 16 226 3.0E-78
9 g11466.t4 SUPERFAMILY SSF57997 Tropomyosin 11 226 4.33E-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.

Raw TPM values