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.t71 isoform g11466.t71 16400669 16404672
chr_1 g11466 g11466.t71 exon g11466.t71.exon1 16400669 16400691
chr_1 g11466 g11466.t71 cds g11466.t71.CDS1 16400671 16400691
chr_1 g11466 g11466.t71 exon g11466.t71.exon2 16400819 16400894
chr_1 g11466 g11466.t71 cds g11466.t71.CDS2 16400819 16400894
chr_1 g11466 g11466.t71 exon g11466.t71.exon3 16401559 16401629
chr_1 g11466 g11466.t71 cds g11466.t71.CDS3 16401559 16401629
chr_1 g11466 g11466.t71 exon g11466.t71.exon4 16403142 16403259
chr_1 g11466 g11466.t71 cds g11466.t71.CDS4 16403142 16403259
chr_1 g11466 g11466.t71 exon g11466.t71.exon5 16403395 16403528
chr_1 g11466 g11466.t71 cds g11466.t71.CDS5 16403395 16403528
chr_1 g11466 g11466.t71 exon g11466.t71.exon6 16404204 16404672
chr_1 g11466 g11466.t71 cds g11466.t71.CDS6 16404204 16404347
chr_1 g11466 g11466.t71 TSS g11466.t71 16404668 16404668
chr_1 g11466 g11466.t71 TTS g11466.t71 NA NA

Sequences

>g11466.t71 Gene=g11466 Length=891
AATTAGGTTTCGCCCATTTTTTTATTGATGACTTAAATCATTCCGCGAGTGAGTTTTAAG
TAAATTAAAGTGATAAATAACAAATATTAATTAATTTCAATCTTTTCCTCACTATATTTG
ATCATTAATAATTCGATTTATCTTGGTTATAGTTGTAAAATTTTCAAGTTACACTGAAAA
TTTTGTATTTTAAAAAAGAAGAAGTATTAGCAATTGAGCGAAAAAAATTTGAGTTTTGCG
GTGTGGTGTTCTAATTTTTAACTAAGTAAAAAAGAAAAAAATATTTTTTAAGTGAAATTT
AATACTAAAGAAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGA
TGTTCTCAAGAAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATG
TGAAGAATTTAATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGA
AGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGA
GCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGA
ACGAATAAGAAAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCT
AGAAGCTCAATTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGA
GGTCGCCAGAAAATTAGTTTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGA
ATTAAGCGAAAGCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTT
GAAGTCATTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGAAGAATA

>g11466.t71 Gene=g11466 Length=188
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEVARKLVLMEQDLERSEEKVELSESKIVELEEELRVVGNNLKSLEVSEE
KANQREEE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11466.t71 Coils Coil Coil 11 107 -
12 g11466.t71 Coils Coil Coil 109 178 -
10 g11466.t71 Gene3D G3DSA:1.20.5.340 - 8 107 7.7E-15
9 g11466.t71 Gene3D G3DSA:1.20.5.340 - 127 188 1.6E-6
2 g11466.t71 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 12 188 1.8E-64
3 g11466.t71 PANTHER PTHR19269 TROPOMYOSIN 12 188 1.8E-64
6 g11466.t71 PRINTS PR00194 Tropomyosin signature 52 69 5.4E-40
4 g11466.t71 PRINTS PR00194 Tropomyosin signature 88 108 5.4E-40
7 g11466.t71 PRINTS PR00194 Tropomyosin signature 113 141 5.4E-40
5 g11466.t71 PRINTS PR00194 Tropomyosin signature 143 166 5.4E-40
1 g11466.t71 Pfam PF00261 Tropomyosin 16 188 4.2E-63
8 g11466.t71 SUPERFAMILY SSF57997 Tropomyosin 11 188 5.61E-49

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