Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t82 isoform g11466.t82 16402266 16407046
chr_1 g11466 g11466.t82 exon g11466.t82.exon1 16402266 16402962
chr_1 g11466 g11466.t82 exon g11466.t82.exon2 16403391 16403528
chr_1 g11466 g11466.t82 cds g11466.t82.CDS1 16403391 16403528
chr_1 g11466 g11466.t82 exon g11466.t82.exon3 16406585 16406868
chr_1 g11466 g11466.t82 cds g11466.t82.CDS2 16406585 16406824
chr_1 g11466 g11466.t82 exon g11466.t82.exon4 16407017 16407046
chr_1 g11466 g11466.t82 TSS g11466.t82 16407060 16407060
chr_1 g11466 g11466.t82 TTS g11466.t82 NA NA

Sequences

>g11466.t82 Gene=g11466 Length=1149
ACTGTTCAAGTCGCGGATTCAGATTCAAGTTCTCTGGTGCTTTCGTAATACCGTAGTAAA
AACACATTACCAAAATGGATGCGATTAAGAAAAAAATGCAAGCAATGAAGCTTGAGAAGG
ATAACGCATTAGATCGCGCCCTTCTCTGTGAACAGCAAGCTCGTGATGCAAACACACGTG
CTGAAAAGGCCGAAGAAGAGGCCCGCACATTGCAAAAGAAGATCCAAACAATTGAAAATG
ATTTGGATCAGACACAAGAACAAGAGACTCTTGTTAATGGAAAGCTTGAAGAAAAAGAAA
AGGCACTTCAAAATGCTGAATCAGAAGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGG
AAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAG
CATCAGCTGCTGCTGATGAATCTGAACGGTAATGCCCGTAAAGTTCTTGAAAACCGTTCA
CTTGCCGATGAAGAGCGTATGGATGCTCTTGAAAATCAATTGAAGGAAGCTCGCTTCCTC
GCTGAAGAAGCTGACAAGAAATACGATGAGGTGCAAAAACTAGACAAAATAACTTGACTC
TAATAACTCTAAATAATTTTTTTCCCATTAATAACAACAATGATGATGTTTTTTTCTCTT
TTTGTATTCGCAATACTGTTTTGGAATGAGAAAGAGTGATAAATCACTTGCCTTAATAAC
TCAAGAGTTAGGAACTTTTTAAGCAACCAAGAATATGCCTAAAACAAGAACGATAGATAT
CTATACATATTTAAAAACGAAAACAATGTTCTTGATGTAATATTTGATGACTAAAACATA
ATTACATACTAATTTTTTTCAACAATTTCATAATAAATTATTATTTCATTTTTTAAATGC
ATTGCATTAAATATTTGATCTAATTTTTATTAAAAAAATTATTGTAAAAGAATAAAATTT
ATCAATTCAAAAAAGACTAATTTTTTCTGCTATACATCTTTTATGAGATTTATCTGTCAT
CTTTGAAATCTTTCAGGAAACTTGCGTTAATTGTTCACAAAGATGGCAGATTGTTGTGGA
AATAATTTCACCTCAATTAATATTTCATCTTCAAAAGATTTTAATTAACATTTTCTCTTT
TGAGAAATG

>g11466.t82 Gene=g11466 Length=125
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESER

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11466.t82 Coils Coil Coil 1 125 -
7 g11466.t82 Gene3D G3DSA:1.20.5.340 - 1 78 3.5E-29
6 g11466.t82 Gene3D G3DSA:1.20.5.340 - 79 123 8.8E-7
5 g11466.t82 MobiDBLite mobidb-lite consensus disorder prediction 106 125 -
2 g11466.t82 PANTHER PTHR19269:SF53 TROPOMYOSIN-2 1 125 1.1E-37
3 g11466.t82 PANTHER PTHR19269 TROPOMYOSIN 1 125 1.1E-37
1 g11466.t82 Pfam PF12718 Tropomyosin like 7 125 2.7E-26
4 g11466.t82 SUPERFAMILY SSF57997 Tropomyosin 1 125 2.51E-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