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.t5 isoform g11466.t5 16396543 16404672
chr_1 g11466 g11466.t5 exon g11466.t5.exon1 16396543 16396907
chr_1 g11466 g11466.t5 cds g11466.t5.CDS1 16396825 16396907
chr_1 g11466 g11466.t5 exon g11466.t5.exon2 16399504 16399573
chr_1 g11466 g11466.t5 cds g11466.t5.CDS2 16399504 16399573
chr_1 g11466 g11466.t5 exon g11466.t5.exon3 16400314 16400376
chr_1 g11466 g11466.t5 cds g11466.t5.CDS3 16400314 16400376
chr_1 g11466 g11466.t5 exon g11466.t5.exon4 16400819 16400894
chr_1 g11466 g11466.t5 cds g11466.t5.CDS4 16400819 16400894
chr_1 g11466 g11466.t5 exon g11466.t5.exon5 16401559 16401629
chr_1 g11466 g11466.t5 cds g11466.t5.CDS5 16401559 16401629
chr_1 g11466 g11466.t5 exon g11466.t5.exon6 16403142 16403259
chr_1 g11466 g11466.t5 cds g11466.t5.CDS6 16403142 16403259
chr_1 g11466 g11466.t5 exon g11466.t5.exon7 16403395 16403528
chr_1 g11466 g11466.t5 cds g11466.t5.CDS7 16403395 16403528
chr_1 g11466 g11466.t5 exon g11466.t5.exon8 16404204 16404672
chr_1 g11466 g11466.t5 cds g11466.t5.CDS8 16404204 16404347
chr_1 g11466 g11466.t5 TSS g11466.t5 16404668 16404668
chr_1 g11466 g11466.t5 TTS g11466.t5 NA NA

Sequences

>g11466.t5 Gene=g11466 Length=1366
AATTAGGTTTCGCCCATTTTTTTATTGATGACTTAAATCATTCCGCGAGTGAGTTTTAAG
TAAATTAAAGTGATAAATAACAAATATTAATTAATTTCAATCTTTTCCTCACTATATTTG
ATCATTAATAATTCGATTTATCTTGGTTATAGTTGTAAAATTTTCAAGTTACACTGAAAA
TTTTGTATTTTAAAAAAGAAGAAGTATTAGCAATTGAGCGAAAAAAATTTGAGTTTTGCG
GTGTGGTGTTCTAATTTTTAACTAAGTAAAAAAGAAAAAAATATTTTTTAAGTGAAATTT
AATACTAAAGAAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGA
TGTTCTCAAGAAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATG
TGAAGAATTTAATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGA
AGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGA
GCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGA
ACGAATAAGAAAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCT
AGAAGCTCAATTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGA
GGTCGCCAGAAAATTAGTTTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGA
ATTAAGCGAAAGCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTT
GAAGTCATTGGAAGTGTCAGAAGAGAAGGCAACACAAAGGGAGGAGACGTTTGAAGGTCA
AGTGAGAATACTGGAAGGACACTTAAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACG
TTCAGTTCAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGAAGAATTGGTACAGGAAAG
GTCAAAGTTCAAAGCAGTAGCAAATCAACTTGATCTCACTTATCATGAACTTCATGGATG
CTAAAGGTTAAAGACAAATCAAAAGGAAAATCACTCGCCTCGAGCATGCTAAATATTTTT
TATATTTTTCGTTTCACTCTACATTCCCAAAAAGAAGATAATGCATTTAAAGCAGTTTGT
ACTTCATTTTTTTCTTGCTTATAATTATCATTTAAAACATTCAAATTTTGAAATATAAAA
ATATTAAGAAAGTAATTCAATGTTTTTACTTTGATTTAAGATCAAATTGCTTAAAACCGT
ATTAAAAGTGCTTAAAAATAAAAAAATTTCAATTGATGAATGCTAA

>g11466.t5 Gene=g11466 Length=252
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEVARKLVLMEQDLERSEEKVELSESKIVELEEELRVVGNNLKSLEVSEE
KATQREETFEGQVRILEGHLKEAEARAEFAERSVQKLQKEVDRLEEELVQERSKFKAVAN
QLDLTYHELHGC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g11466.t5 Coils Coil Coil 11 107 -
14 g11466.t5 Coils Coil Coil 109 178 -
15 g11466.t5 Coils Coil Coil 193 241 -
11 g11466.t5 Gene3D G3DSA:1.20.5.340 - 8 107 1.5E-14
12 g11466.t5 Gene3D G3DSA:1.20.5.340 - 127 227 1.7E-18
2 g11466.t5 PANTHER PTHR19269:SF45 TROPOMYOSIN-1, ISOFORMS 33/34 12 250 1.2E-86
3 g11466.t5 PANTHER PTHR19269 TROPOMYOSIN 12 250 1.2E-86
7 g11466.t5 PRINTS PR00194 Tropomyosin signature 52 69 5.1E-54
5 g11466.t5 PRINTS PR00194 Tropomyosin signature 88 108 5.1E-54
8 g11466.t5 PRINTS PR00194 Tropomyosin signature 113 141 5.1E-54
6 g11466.t5 PRINTS PR00194 Tropomyosin signature 143 166 5.1E-54
4 g11466.t5 PRINTS PR00194 Tropomyosin signature 199 224 5.1E-54
1 g11466.t5 Pfam PF00261 Tropomyosin 16 250 7.5E-88
10 g11466.t5 ProSitePatterns PS00326 Tropomyosins signature. 200 208 -
9 g11466.t5 SUPERFAMILY SSF57997 Tropomyosin 11 251 3.27E-70

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