Gene loci information

Transcript annotation

  • This transcript has been annotated as Tropomyosin.

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.t74 isoform g11466.t74 16401951 16407076
chr_1 g11466 g11466.t74 exon g11466.t74.exon1 16401951 16401971
chr_1 g11466 g11466.t74 cds g11466.t74.CDS1 16401951 16401971
chr_1 g11466 g11466.t74 exon g11466.t74.exon2 16402845 16402962
chr_1 g11466 g11466.t74 cds g11466.t74.CDS2 16402845 16402962
chr_1 g11466 g11466.t74 exon g11466.t74.exon3 16403395 16403528
chr_1 g11466 g11466.t74 cds g11466.t74.CDS3 16403395 16403528
chr_1 g11466 g11466.t74 exon g11466.t74.exon4 16406585 16406868
chr_1 g11466 g11466.t74 cds g11466.t74.CDS4 16406585 16406824
chr_1 g11466 g11466.t74 exon g11466.t74.exon5 16407017 16407076
chr_1 g11466 g11466.t74 TSS g11466.t74 16407060 16407060
chr_1 g11466 g11466.t74 TTS g11466.t74 NA NA

Sequences

>g11466.t74 Gene=g11466 Length=617
AGTAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGT
TCTCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGA
AAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTG
AACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACAT
TGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTC
TTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCG
CTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTT
TGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGTG
CCCGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTTGAAA
ATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAGGTTG
CACGTAAATTAGCTATG

>g11466.t74 Gene=g11466 Length=171
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11466.t74 Coils Coil Coil 1 168 -
10 g11466.t74 Gene3D G3DSA:1.20.5.340 - 1 95 2.5E-36
9 g11466.t74 Gene3D G3DSA:1.20.5.340 - 96 139 6.5E-6
8 g11466.t74 MobiDBLite mobidb-lite consensus disorder prediction 109 134 -
7 g11466.t74 MobiDBLite mobidb-lite consensus disorder prediction 118 134 -
2 g11466.t74 PANTHER PTHR19269 TROPOMYOSIN 1 171 4.2E-60
3 g11466.t74 PRINTS PR00194 Tropomyosin signature 84 101 1.9E-30
5 g11466.t74 PRINTS PR00194 Tropomyosin signature 120 140 1.9E-30
4 g11466.t74 PRINTS PR00194 Tropomyosin signature 145 171 1.9E-30
1 g11466.t74 Pfam PF00261 Tropomyosin 48 171 2.9E-43
6 g11466.t74 SUPERFAMILY SSF57997 Tropomyosin 1 171 1.12E-54

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