General information for g11466.t48
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tropomyosin.
Parent gene
- The parent gene g11466 is located on chr_1: 16405874..16407076 (- 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 | g11466 | g11466.t48 | TTS | g11466.t48 | 16397069 | 16397069 |
| chr_1 | g11466 | g11466.t48 | isoform | g11466.t48 | 16397451 | 16407074 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon1 | 16397451 | 16397553 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS1 | 16397468 | 16397553 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon3 | 16400629 | 16400691 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS3 | 16400629 | 16400691 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon4 | 16400834 | 16400894 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS4 | 16400834 | 16400894 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon5 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS5 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon6 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS6 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon7 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS7 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon8 | 16406585 | 16406868 |
| chr_1 | g11466 | g11466.t48 | cds | g11466.t48.CDS8 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t48 | exon | g11466.t48.exon9 | 16407017 | 16407074 |
| chr_1 | g11466 | g11466.t48 | TSS | g11466.t48 | 16407060 | 16407060 |
Sequences
>g11466.t48 Gene=g11466 Length=962
TAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGTTC
TCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGAAA
AAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTGAA
CAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACATTG
CAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTCTT
GTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCGCT
GCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTTTG
GCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGTGCC
CGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTTGAAAAT
CAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAGGTTGCA
CGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTGCAGAAGCTGGT
GAAGCCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAAGTCA
TTGGAAGCAAATCAACGTGAAGAAGAATATAAGAATCAAATTAAGACTCTTACCACCCGC
CTTAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTTCAGAAATTGCAGAAA
GAAGTCGACAGACTTGAAGATGAGCTTGTTTCCGAAAAGGAGAAATACAGAGAAATTGGA
GACGATCTCGATACCGCTTTTGTGGAACTCATCCTTAAGGAATAAAGGATTTTCGGCCTA
CA
>g11466.t48 Gene=g11466 Length=280
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEAKIVELEEELRVVGNNLKSLEANQREEEYKNQIKTLTTRLKEAEARAEFAERS
VQKLQKEVDRLEDELVSEKEKYREIGDDLDTAFVELILKE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11466.t48 | Coils | Coil | Coil | 1 | 268 | - |
| 12 | g11466.t48 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 95 | 8.3E-36 |
| 11 | g11466.t48 | Gene3D | G3DSA:1.20.5.340 | - | 96 | 139 | 1.5E-5 |
| 10 | g11466.t48 | Gene3D | G3DSA:1.20.5.340 | - | 160 | 254 | 8.4E-20 |
| 2 | g11466.t48 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 277 | 1.9E-115 |
| 4 | g11466.t48 | PRINTS | PR00194 | Tropomyosin signature | 84 | 101 | 8.9E-46 |
| 7 | g11466.t48 | PRINTS | PR00194 | Tropomyosin signature | 120 | 140 | 8.9E-46 |
| 3 | g11466.t48 | PRINTS | PR00194 | Tropomyosin signature | 145 | 173 | 8.9E-46 |
| 5 | g11466.t48 | PRINTS | PR00194 | Tropomyosin signature | 175 | 198 | 8.9E-46 |
| 6 | g11466.t48 | PRINTS | PR00194 | Tropomyosin signature | 233 | 258 | 8.9E-46 |
| 1 | g11466.t48 | Pfam | PF00261 | Tropomyosin | 48 | 277 | 5.2E-88 |
| 9 | g11466.t48 | ProSitePatterns | PS00326 | Tropomyosins signature. | 227 | 235 | - |
| 8 | g11466.t48 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 276 | 1.01E-89 |
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 transcript has been annotated with K10373 (tropomyosin 1)
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. There were no conditions that were differentially expressed