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.t6 isoform g11464.t6 16389951 16394191
chr_1 g11464 g11464.t6 exon g11464.t6.exon1 16389951 16390028
chr_1 g11464 g11464.t6 TTS g11464.t6 16389991 16389991
chr_1 g11464 g11464.t6 exon g11464.t6.exon2 16390115 16390388
chr_1 g11464 g11464.t6 cds g11464.t6.CDS1 16390306 16390388
chr_1 g11464 g11464.t6 exon g11464.t6.exon3 16393192 16393369
chr_1 g11464 g11464.t6 cds g11464.t6.CDS2 16393192 16393369
chr_1 g11464 g11464.t6 exon g11464.t6.exon4 16393544 16393763
chr_1 g11464 g11464.t6 cds g11464.t6.CDS3 16393544 16393763
chr_1 g11464 g11464.t6 exon g11464.t6.exon5 16393833 16394191
chr_1 g11464 g11464.t6 cds g11464.t6.CDS4 16393833 16394185
chr_1 g11464 g11464.t6 TSS g11464.t6 16395053 16395053

Sequences

>g11464.t6 Gene=g11464 Length=1109
AAGAAGATGCAAGCAATGAAGCTTGAGAAAGATAATGCTCAAGACAAAGCTGACACCTGC
GAGAATCAAGCCAAGGATGCCAACGCCAAGGCCGCTAAGGTCGAAGAAGAAGTTGCCGAT
TTGATCAAGAAATTGGCTCAAGTTGAAAGCGATTTGGAAGCACACAAGAATGCTTTGGAG
CAAGCCAACAAGGATTTAGAAGAAAAAGAAAAGCTCCTCACAACCACAGAATCAGAAGTT
GCTGCATTAAACAGAAAAGTACAACAGGTTGAAGAAGATTTGGAAAAGTCAGAAGAACGC
TCATCAACTGCTATGCAAAAACTTTTGGAAGCCACACAAGCTGCTGATGAAAATAACCGT
ATGTGCAAGGTATTGGAGAATCGTGCACAGCAAGATGAAGAGCGCATGGATCAATTGACA
AACCAACTTAAAGAAGCACGTCTCCTTGCTGAAGACGCCGATGGTAAATCAGATGAAGTT
TCACGCAAGTTGGCCTTCGTTGAAGATGAATTGGAAGTTGCTGAAGATCGTGTTAAGTCA
GGAGAGGCAAAGATCATGGAACTTGAAGAAGAATTGAAGGTTGTTGGTAACTCATTGAAA
TCATTGGAAGTATCAGAAGAAAAGGCTAACCAGAGAGTTGAAGAATTCAAACGTCAATTG
AAATCATTGACAATCAAACTTAAGGAAGCCGAAAATCGTGCAGAATTGGCTGAGAAGACA
GTCAAGAAACTGCAAAAGGAAGTTGACAGACTTGAAGATGAACTTGGTCTCAACAAAGAC
AGATACAAGTCACTTGCCGATGAAATGGATTCAACCTTTGCTGAATTGGCAGGCTATTAA
ACAATCACCATTGTGTGTGAAATCGAAGCAAAGCGAAAACTGTGCATGTCTTGAAGAACG
TTCTGTAAACAATAACTATTTATTTAAATCACATAAACATGATGTATCTCTTTTTTTTTG
CTATTCAGATCGAATAACTTTTTTTTGTCCAACACGAGAAAGTTACTTTTAGAAATCTCA
TAATGTCTTATCTTTTAAAAAACAGAAATCTTAATAAAGAAACTGTAACAAAAAAATCTT
ATGATGATAGATAGAATTTATAGGAAAAT

>g11464.t6 Gene=g11464 Length=277
MQAMKLEKDNAQDKADTCENQAKDANAKAAKVEEEVADLIKKLAQVESDLEAHKNALEQA
NKDLEEKEKLLTTTESEVAALNRKVQQVEEDLEKSEERSSTAMQKLLEATQAADENNRMC
KVLENRAQQDEERMDQLTNQLKEARLLAEDADGKSDEVSRKLAFVEDELEVAEDRVKSGE
AKIMELEEELKVVGNSLKSLEVSEEKANQRVEEFKRQLKSLTIKLKEAENRAELAEKTVK
KLQKEVDRLEDELGLNKDRYKSLADEMDSTFAELAGY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11464.t6 Coils Coil Coil 1 105 -
13 g11464.t6 Coils Coil Coil 113 266 -
11 g11464.t6 Gene3D G3DSA:1.20.5.340 - 1 72 2.1E-18
12 g11464.t6 Gene3D G3DSA:1.20.5.340 - 73 133 1.4E-8
10 g11464.t6 Gene3D G3DSA:1.20.5.340 - 152 252 2.1E-18
16 g11464.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
2 g11464.t6 PANTHER PTHR19269:SF53 TROPOMYOSIN-2 1 277 2.8E-149
3 g11464.t6 PANTHER PTHR19269 TROPOMYOSIN 1 277 2.8E-149
7 g11464.t6 PRINTS PR00194 Tropomyosin signature 77 94 6.7E-47
4 g11464.t6 PRINTS PR00194 Tropomyosin signature 113 133 6.7E-47
8 g11464.t6 PRINTS PR00194 Tropomyosin signature 138 166 6.7E-47
6 g11464.t6 PRINTS PR00194 Tropomyosin signature 168 191 6.7E-47
5 g11464.t6 PRINTS PR00194 Tropomyosin signature 224 249 6.7E-47
1 g11464.t6 Pfam PF00261 Tropomyosin 41 275 5.4E-76
15 g11464.t6 ProSitePatterns PS00326 Tropomyosins signature. 225 233 -
9 g11464.t6 SUPERFAMILY SSF57997 Tropomyosin 1 276 2.29E-81

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

Pathway

  • This transcript belongs to the following pathways

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