Gene loci information

Transcript annotation

  • This transcript has been annotated as Tropomyosin-1.

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 g11464 g11464.t32 isoform g11464.t32 16393240 16394206
chr_1 g11464 g11464.t32 exon g11464.t32.exon1 16393240 16393369
chr_1 g11464 g11464.t32 cds g11464.t32.CDS1 16393241 16393369
chr_1 g11464 g11464.t32 exon g11464.t32.exon2 16393544 16393763
chr_1 g11464 g11464.t32 cds g11464.t32.CDS2 16393544 16393763
chr_1 g11464 g11464.t32 exon g11464.t32.exon3 16393833 16394206
chr_1 g11464 g11464.t32 cds g11464.t32.CDS3 16393833 16394206
chr_1 g11464 g11464.t32 TSS g11464.t32 16395053 16395053
chr_1 g11464 g11464.t32 TTS g11464.t32 NA NA

Sequences

>g11464.t32 Gene=g11464 Length=724
ATGGACGCCATTAAGAAGAAGATGCAAGCAATGAAGCTTGAGAAAGATAATGCTCAAGAC
AAAGCTGACACCTGCGAGAATCAAGCCAAGGATGCCAACGCCAAGGCCGCTAAGGTCGAA
GAAGAAGTTGCCGATTTGATCAAGAAATTGGCTCAAGTTGAAAGCGATTTGGAAGCACAC
AAGAATGCTTTGGAGCAAGCCAACAAGGATTTAGAAGAAAAAGAAAAGCTCCTCACAACC
ACAGAATCAGAAGTTGCTGCATTAAACAGAAAAGTACAACAGGTTGAAGAAGATTTGGAA
AAGTCAGAAGAACGCTCATCAACTGCTATGCAAAAACTTTTGGAAGCCACACAAGCTGCT
GATGAAAATAACCGTATGTGCAAGGTATTGGAGAATCGTGCACAGCAAGATGAAGAGCGC
ATGGATCAATTGACAAACCAACTTAAAGAAGCACGTCTCCTTGCTGAAGACGCCGATGGT
AAATCAGATGAAGTTTCACGCAAGTTGGCCTTCGTTGAAGATGAATTGGAAGTTGCTGAA
GATCGTGTTAAGTCAGGAGAGGCAAAGATCATGGAACTTGAAGAAGAATTGAAGGTTGTT
GGTAACTCATTGAAATCATTGGAAGTATCAGAAGAAAAGGCTAACCAGAGAGTTGAAGAA
TTCAAACGTCAATTGAAATCATTGACAATCAAACTTAAGGAAGCCGAAAATCGTGCAGAA
TTGG

>g11464.t32 Gene=g11464 Length=241
MDAIKKKMQAMKLEKDNAQDKADTCENQAKDANAKAAKVEEEVADLIKKLAQVESDLEAH
KNALEQANKDLEEKEKLLTTTESEVAALNRKVQQVEEDLEKSEERSSTAMQKLLEATQAA
DENNRMCKVLENRAQQDEERMDQLTNQLKEARLLAEDADGKSDEVSRKLAFVEDELEVAE
DRVKSGEAKIMELEEELKVVGNSLKSLEVSEEKANQRVEEFKRQLKSLTIKLKEAENRAE
L

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11464.t32 Coils Coil Coil 1 112 -
13 g11464.t32 Coils Coil Coil 120 241 -
12 g11464.t32 Gene3D G3DSA:1.20.5.340 - 1 79 3.1E-24
11 g11464.t32 Gene3D G3DSA:1.20.5.340 - 80 140 9.2E-9
10 g11464.t32 Gene3D G3DSA:1.20.5.340 - 159 241 8.5E-13
16 g11464.t32 MobiDBLite mobidb-lite consensus disorder prediction 1 27 -
2 g11464.t32 PANTHER PTHR19269:SF53 TROPOMYOSIN-2 1 240 3.5E-131
3 g11464.t32 PANTHER PTHR19269 TROPOMYOSIN 1 240 3.5E-131
5 g11464.t32 PRINTS PR00194 Tropomyosin signature 84 101 6.1E-39
7 g11464.t32 PRINTS PR00194 Tropomyosin signature 120 140 6.1E-39
4 g11464.t32 PRINTS PR00194 Tropomyosin signature 145 173 6.1E-39
6 g11464.t32 PRINTS PR00194 Tropomyosin signature 175 198 6.1E-39
8 g11464.t32 PRINTS PR00194 Tropomyosin signature 231 241 6.1E-39
1 g11464.t32 Pfam PF00261 Tropomyosin 48 240 9.1E-60
15 g11464.t32 ProSitePatterns PS00326 Tropomyosins signature. 232 240 -
9 g11464.t32 SUPERFAMILY SSF57997 Tropomyosin 1 240 1.96E-71

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