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.t73 isoform g11466.t73 16401563 16404672
chr_1 g11466 g11466.t73 exon g11466.t73.exon1 16401563 16401629
chr_1 g11466 g11466.t73 cds g11466.t73.CDS1 16401564 16401629
chr_1 g11466 g11466.t73 exon g11466.t73.exon2 16403142 16403259
chr_1 g11466 g11466.t73 cds g11466.t73.CDS2 16403142 16403259
chr_1 g11466 g11466.t73 exon g11466.t73.exon3 16403395 16403528
chr_1 g11466 g11466.t73 cds g11466.t73.CDS3 16403395 16403528
chr_1 g11466 g11466.t73 exon g11466.t73.exon4 16404204 16404672
chr_1 g11466 g11466.t73 cds g11466.t73.CDS4 16404204 16404347
chr_1 g11466 g11466.t73 TSS g11466.t73 16404668 16404668
chr_1 g11466 g11466.t73 TTS g11466.t73 NA NA

Sequences

>g11466.t73 Gene=g11466 Length=788
AATTAGGTTTCGCCCATTTTTTTATTGATGACTTAAATCATTCCGCGAGTGAGTTTTAAG
TAAATTAAAGTGATAAATAACAAATATTAATTAATTTCAATCTTTTCCTCACTATATTTG
ATCATTAATAATTCGATTTATCTTGGTTATAGTTGTAAAATTTTCAAGTTACACTGAAAA
TTTTGTATTTTAAAAAAGAAGAAGTATTAGCAATTGAGCGAAAAAAATTTGAGTTTTGCG
GTGTGGTGTTCTAATTTTTAACTAAGTAAAAAAGAAAAAAATATTTTTTAAGTGAAATTT
AATACTAAAGAAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGA
TGTTCTCAAGAAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATG
TGAAGAATTTAATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGA
AGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGA
GCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGA
ACGAATAAGAAAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCT
AGAAGCTCAATTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGA
GGTCGCCAGAAAATTAGTTTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGA
ATTAAGCG

>g11466.t73 Gene=g11466 Length=154
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEVARKLVLMEQDLERSEEKVELS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11466.t73 Coils Coil Coil 11 107 -
11 g11466.t73 Coils Coil Coil 109 154 -
9 g11466.t73 Gene3D G3DSA:1.20.5.340 - 8 107 4.5E-15
2 g11466.t73 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 12 152 3.5E-46
3 g11466.t73 PANTHER PTHR19269 TROPOMYOSIN 12 152 3.5E-46
6 g11466.t73 PRINTS PR00194 Tropomyosin signature 52 69 2.6E-33
4 g11466.t73 PRINTS PR00194 Tropomyosin signature 88 108 2.6E-33
7 g11466.t73 PRINTS PR00194 Tropomyosin signature 113 141 2.6E-33
5 g11466.t73 PRINTS PR00194 Tropomyosin signature 143 154 2.6E-33
1 g11466.t73 Pfam PF00261 Tropomyosin 16 153 6.4E-47
8 g11466.t73 SUPERFAMILY SSF57997 Tropomyosin 11 153 2.09E-36

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