General information for g11466.t56
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Tropomyosin-1, isoforms 9A/A/B.
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.t56 | TTS | g11466.t56 | 16398326 | 16398326 |
| chr_1 | g11466 | g11466.t56 | isoform | g11466.t56 | 16399209 | 16404362 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon1 | 16399209 | 16399291 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon3 | 16400314 | 16400404 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon4 | 16401536 | 16401621 |
| chr_1 | g11466 | g11466.t56 | cds | g11466.t56.CDS1 | 16401571 | 16401621 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon5 | 16403142 | 16403259 |
| chr_1 | g11466 | g11466.t56 | cds | g11466.t56.CDS2 | 16403142 | 16403259 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon6 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t56 | cds | g11466.t56.CDS3 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t56 | exon | g11466.t56.exon7 | 16404204 | 16404362 |
| chr_1 | g11466 | g11466.t56 | cds | g11466.t56.CDS4 | 16404204 | 16404347 |
| chr_1 | g11466 | g11466.t56 | TSS | g11466.t56 | 16404668 | 16404668 |
Sequences
>g11466.t56 Gene=g11466 Length=741
AAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGATGTTCTCAAG
AAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATGTGAAGAATTT
AATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGAAGTCGCTGCT
TTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCA
TCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGAATAAGA
AAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCTAGAAGCTCAA
TTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGAGAAAATTAGT
TTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGAATTAAGCGAAAGGTTTGC
TTTTTTTCTAACACGAAGAAAATCAAATAATTTGGACATAACCAGGCAACACAAAGGGAG
GAGACGTTTGAAGGTCAAGTGAGAATACTGGAAGGACACTTAAAGGAGGCTGAAGCCAGA
GCCGAATTTGCTGAACGTTCAGTTCAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGAT
GAATTGTTAAATGAGCGTGCACGAAACAAGATGCTCCAGGAAGAAATGGAAGCGACACTT
CATGATATTCAGAATATGTAA
>g11466.t56 Gene=g11466 Length=148
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEKISFDGARFRAFRRKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11466.t56 | Coils | Coil | Coil | 11 | 107 | - |
| 10 | g11466.t56 | Coils | Coil | Coil | 109 | 129 | - |
| 8 | g11466.t56 | Gene3D | G3DSA:1.20.5.340 | - | 8 | 107 | 4.0E-15 |
| 2 | g11466.t56 | PANTHER | PTHR19269:SF45 | TROPOMYOSIN-1, ISOFORMS 33/34 | 12 | 132 | 1.6E-37 |
| 3 | g11466.t56 | PANTHER | PTHR19269 | TROPOMYOSIN | 12 | 132 | 1.6E-37 |
| 5 | g11466.t56 | PRINTS | PR00194 | Tropomyosin signature | 52 | 69 | 2.3E-19 |
| 4 | g11466.t56 | PRINTS | PR00194 | Tropomyosin signature | 88 | 108 | 2.3E-19 |
| 6 | g11466.t56 | PRINTS | PR00194 | Tropomyosin signature | 113 | 141 | 2.3E-19 |
| 1 | g11466.t56 | Pfam | PF00261 | Tropomyosin | 16 | 132 | 1.3E-37 |
| 7 | g11466.t56 | SUPERFAMILY | SSF57997 | Tropomyosin | 11 | 133 | 4.41E-29 |
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.
