Gene loci information

Transcript annotation

  • This transcript has been annotated as Tropomyosin-2.

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.t16 isoform g11464.t16 16389951 16395040
chr_1 g11464 g11464.t16 exon g11464.t16.exon1 16389951 16390388
chr_1 g11464 g11464.t16 TTS g11464.t16 16389991 16389991
chr_1 g11464 g11464.t16 exon g11464.t16.exon2 16391592 16392401
chr_1 g11464 g11464.t16 cds g11464.t16.CDS1 16392319 16392401
chr_1 g11464 g11464.t16 exon g11464.t16.exon3 16393192 16393369
chr_1 g11464 g11464.t16 cds g11464.t16.CDS2 16393192 16393369
chr_1 g11464 g11464.t16 exon g11464.t16.exon4 16393544 16393763
chr_1 g11464 g11464.t16 cds g11464.t16.CDS3 16393544 16393763
chr_1 g11464 g11464.t16 exon g11464.t16.exon5 16393833 16394255
chr_1 g11464 g11464.t16 cds g11464.t16.CDS4 16393833 16394206
chr_1 g11464 g11464.t16 exon g11464.t16.exon6 16395006 16395040
chr_1 g11464 g11464.t16 TSS g11464.t16 16395053 16395053

Sequences

>g11464.t16 Gene=g11464 Length=2104
ATTTTGTGTTGCGAGGATCTTTATAGAGCGCTCAGTTATTTTCATTAGCATTATTTTCGA
GTAGAACAAAGAAAAAGCCTAAAAATGGACGCCATTAAGAAGAAGATGCAAGCAATGAAG
CTTGAGAAAGATAATGCTCAAGACAAAGCTGACACCTGCGAGAATCAAGCCAAGGATGCC
AACGCCAAGGCCGCTAAGGTCGAAGAAGAAGTTGCCGATTTGATCAAGAAATTGGCTCAA
GTTGAAAGCGATTTGGAAGCACACAAGAATGCTTTGGAGCAAGCCAACAAGGATTTAGAA
GAAAAAGAAAAGCTCCTCACAACCACAGAATCAGAAGTTGCTGCATTAAACAGAAAAGTA
CAACAGGTTGAAGAAGATTTGGAAAAGTCAGAAGAACGCTCATCAACTGCTATGCAAAAA
CTTTTGGAAGCCACACAAGCTGCTGATGAAAATAACCGTATGTGCAAGGTATTGGAGAAT
CGTGCACAGCAAGATGAAGAGCGCATGGATCAATTGACAAACCAACTTAAAGAAGCACGT
CTCCTTGCTGAAGACGCCGATGGTAAATCAGATGAAGTTTCACGCAAGTTGGCCTTCGTT
GAAGATGAATTGGAAGTTGCTGAAGATCGTGTTAAGTCAGGAGAGGCAAAGATCATGGAA
CTTGAAGAAGAATTGAAGGTTGTTGGTAACTCATTGAAATCATTGGAAGTATCAGAAGAA
AAGGCTAACCAGAGAGTTGAAGAATTCAAACGTCAATTGAAATCATTGACAATCAAACTT
AAGGAAGCCGAAAATCGTGCAGAATTGGCTGAGAAGACAGTCAAGAAACTGCAAAAGGAA
GTTGACAGACTTGAAGACAAGCTCGCAGTTCAAAAAGAAACATACAATGCTATCTGCACG
GATATGGACACTACCTTTGCCGAAATGGCAGGATTTTAAATCTCATTTTAAAGTTCATAA
AATTTCTCTTTTGTTCACTTATAAATCCCATTTCCAACATAATCTTTGGTCCGATTTTTA
CTACATTAAAATCCAACCATAAACAAACAATCTCAAAAATTAGTAAAACAATAATGATAC
ATCAATGTCATATATATATATATATACACTATGATTGTATATATTTTATATAAATATCTT
ATATTTATATTTTAACTCTTTCTTTTCCAACCATTCACAAGACAGAACTCAACTCATGAA
TCACTTGAATATCTTAGATTGTTTCTCTCCATATAAACAAGACTCTTTTGAGGTCTCTCT
CTATCCTTCAAGACAATAGATCATGATATATTATCGATTTAAATCATCATTATTAACCAT
TCTTCCTATATCACATACATACATACACACACAAACATTTTATATCTCTTTGTACTGCTG
TATTAATATAGAATTGCAAATAATGAGCAAATGATAATATAAATTTATTGGCTTTTACTA
AATGCTATGACTAAAAACTTATATTTTCTAACATCAATATCAACAATTATCCTTTTCTAA
ATTCAAACATCATCATGAAAAATAAACATTAAAACTACTGAAAGTACAACGATAATGAGG
GCGATGGCTAATGGCTACCAACTGGAATTCAATTAAAATCAAATAATATTTTAAGCCAAA
AAAATAATCAAACTGCTGCTATTATTTTTAAAAAGCCTGACTTAAGATGAACTTGGTCTC
AACAAAGACAGATACAAGTCACTTGCCGATGAAATGGATTCAACCTTTGCTGAATTGGCA
GGCTATTAAACAATCACCATTGTGTGTGAAATCGAAGCAAAGCGAAAACTGTGCATGTCT
TGAAGAACGTTCTGTAAACAATAACTATTTATTTAAATCACATAAACATGATGTATCTCT
TTTTTTTTGCTATTCAGATCGAATAACTTTTTTTTGTCCAACACGAGAAAGTTACTTTTA
GAAATCTCATAATGTCTTATTTTACAATACAATAATTGAAAAAGTATCAAAAGTTCTAAC
ATTTTTTATTGTTTTATGATGGAAAGAAAATTTTTGTGCTCTCTCTCTTTTAAAAAACAG
AAATCTTAATAAAGAAACTGTAACAAAAAAATCTTATGATGATAGATAGAATTTATAGGA
AAAT

>g11464.t16 Gene=g11464 Length=284
MDAIKKKMQAMKLEKDNAQDKADTCENQAKDANAKAAKVEEEVADLIKKLAQVESDLEAH
KNALEQANKDLEEKEKLLTTTESEVAALNRKVQQVEEDLEKSEERSSTAMQKLLEATQAA
DENNRMCKVLENRAQQDEERMDQLTNQLKEARLLAEDADGKSDEVSRKLAFVEDELEVAE
DRVKSGEAKIMELEEELKVVGNSLKSLEVSEEKANQRVEEFKRQLKSLTIKLKEAENRAE
LAEKTVKKLQKEVDRLEDKLAVQKETYNAICTDMDTTFAEMAGF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11464.t16 Coils Coil Coil 1 112 -
13 g11464.t16 Coils Coil Coil 120 266 -
12 g11464.t16 Gene3D G3DSA:1.20.5.340 - 1 79 4.4E-24
11 g11464.t16 Gene3D G3DSA:1.20.5.340 - 80 139 1.2E-8
10 g11464.t16 Gene3D G3DSA:1.20.5.340 - 159 259 4.0E-18
16 g11464.t16 MobiDBLite mobidb-lite consensus disorder prediction 1 27 -
2 g11464.t16 PANTHER PTHR19269:SF53 TROPOMYOSIN-2 1 283 2.9E-153
3 g11464.t16 PANTHER PTHR19269 TROPOMYOSIN 1 283 2.9E-153
6 g11464.t16 PRINTS PR00194 Tropomyosin signature 84 101 7.5E-47
8 g11464.t16 PRINTS PR00194 Tropomyosin signature 120 140 7.5E-47
4 g11464.t16 PRINTS PR00194 Tropomyosin signature 145 173 7.5E-47
7 g11464.t16 PRINTS PR00194 Tropomyosin signature 175 198 7.5E-47
5 g11464.t16 PRINTS PR00194 Tropomyosin signature 231 256 7.5E-47
1 g11464.t16 Pfam PF00261 Tropomyosin 48 282 1.0E-74
15 g11464.t16 ProSitePatterns PS00326 Tropomyosins signature. 232 240 -
9 g11464.t16 SUPERFAMILY SSF57997 Tropomyosin 1 283 1.77E-85

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