General information for g11464.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tropomyosin-1.
Parent gene
- The parent gene g11464 is located on chr_1: 16393544..16395040 (- strand)
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.t28 | TTS | g11464.t28 | 16389991 | 16389991 |
| chr_1 | g11464 | g11464.t28 | isoform | g11464.t28 | 16390306 | 16395040 |
| chr_1 | g11464 | g11464.t28 | exon | g11464.t28.exon1 | 16390306 | 16390388 |
| chr_1 | g11464 | g11464.t28 | cds | g11464.t28.CDS1 | 16390306 | 16390388 |
| chr_1 | g11464 | g11464.t28 | exon | g11464.t28.exon2 | 16393192 | 16393369 |
| chr_1 | g11464 | g11464.t28 | cds | g11464.t28.CDS2 | 16393192 | 16393369 |
| chr_1 | g11464 | g11464.t28 | exon | g11464.t28.exon3 | 16393544 | 16393802 |
| chr_1 | g11464 | g11464.t28 | cds | g11464.t28.CDS3 | 16393544 | 16393717 |
| chr_1 | g11464 | g11464.t28 | exon | g11464.t28.exon4 | 16393934 | 16394255 |
| chr_1 | g11464 | g11464.t28 | exon | g11464.t28.exon5 | 16395006 | 16395040 |
| chr_1 | g11464 | g11464.t28 | TSS | g11464.t28 | 16395053 | 16395053 |
Sequences
>g11464.t28 Gene=g11464 Length=877
ATTTTGTGTTGCGAGGATCTTTATAGAGCGCTCAGTTATTTTCATTAGCATTATTTTCGA
GTAGAACAAAGAAAAAGCCTAAAAATGGACGCCATTAAGAAGAAGATGCAAGCAATGAAG
CTTGAGAAAGATAATGCTCAAGACAAAGCTGACACCTGCGAGAATCAAGCCAAGGATGCC
AACGCCAAGGCCGCTAAGGTCGAAGAAGAAGTTGCCGATTTGATCAAGAAATTGGCTCAA
GTTGAAAGCGATTTGGAAGCACACAAGAATGCTTTGGAGCAAGCCAACAAGGATTTAGAA
GAAAAAGAAAAGCTCCTCACAACCACAGAATCAGAAGTTGCTGCATTAAACAGAAAATCA
AATTTTAATAATAATTTATACTTTGTAATATTTCAGTATGTGCAAGGTATTGGAGAATCG
TGCACAGCAAGATGAAGAGCGCATGGATCAATTGACAAACCAACTTAAAGAAGCACGTCT
CCTTGCTGAAGACGCCGATGGTAAATCAGATGAAGTTTCACGCAAGTTGGCCTTCGTTGA
AGATGAATTGGAAGTTGCTGAAGATCGTGTTAAGTCAGGAGAGGCAAAGATCATGGAACT
TGAAGAAGAATTGAAGGTTGTTGGTAACTCATTGAAATCATTGGAAGTATCAGAAGAAAA
GGCTAACCAGAGAGTTGAAGAATTCAAACGTCAATTGAAATCATTGACAATCAAACTTAA
GGAAGCCGAAAATCGTGCAGAATTGGCTGAGAAGACAGTCAAGAAACTGCAAAAGGAAGT
TGACAGACTTGAAGATGAACTTGGTCTCAACAAAGACAGATACAAGTCACTTGCCGATGA
AATGGATTCAACCTTTGCTGAATTGGCAGGCTATTAA
>g11464.t28 Gene=g11464 Length=144
MDQLTNQLKEARLLAEDADGKSDEVSRKLAFVEDELEVAEDRVKSGEAKIMELEEELKVV
GNSLKSLEVSEEKANQRVEEFKRQLKSLTIKLKEAENRAELAEKTVKKLQKEVDRLEDEL
GLNKDRYKSLADEMDSTFAELAGY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11464.t28 | Coils | Coil | Coil | 1 | 133 | - |
| 9 | g11464.t28 | Gene3D | G3DSA:1.20.5.340 | - | 19 | 119 | 3.8E-19 |
| 2 | g11464.t28 | PANTHER | PTHR19269:SF53 | TROPOMYOSIN-2 | 1 | 144 | 5.6E-79 |
| 3 | g11464.t28 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 144 | 5.6E-79 |
| 6 | g11464.t28 | PRINTS | PR00194 | Tropomyosin signature | 5 | 33 | 9.0E-30 |
| 5 | g11464.t28 | PRINTS | PR00194 | Tropomyosin signature | 35 | 58 | 9.0E-30 |
| 4 | g11464.t28 | PRINTS | PR00194 | Tropomyosin signature | 91 | 116 | 9.0E-30 |
| 1 | g11464.t28 | Pfam | PF00261 | Tropomyosin | 1 | 142 | 2.0E-48 |
| 8 | g11464.t28 | ProSitePatterns | PS00326 | Tropomyosins signature. | 92 | 100 | - |
| 7 | g11464.t28 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 144 | 1.42E-44 |
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.
