General information for g11466.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t20 | isoform | g11466.t20 | 16397067 | 16406824 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon1 | 16397067 | 16397553 |
| chr_1 | g11466 | g11466.t20 | TTS | g11466.t20 | 16397069 | 16397069 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon2 | 16399504 | 16399562 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon3 | 16400629 | 16400691 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon4 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon5 | 16401908 | 16401971 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon6 | 16402845 | 16402951 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon7 | 16403391 | 16403528 |
| chr_1 | g11466 | g11466.t20 | cds | g11466.t20.CDS1 | 16403391 | 16403528 |
| chr_1 | g11466 | g11466.t20 | exon | g11466.t20.exon8 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t20 | cds | g11466.t20.CDS2 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t20 | TSS | g11466.t20 | 16407060 | 16407060 |
Sequences
>g11466.t20 Gene=g11466 Length=1234
ATGGATGCGATTAAGAAAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGAT
CGCGCCCTTCTCTGTGAACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAA
GAAGAGGCCCGCACATTGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACA
CAAGAACAAGAGACTCTTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAAT
GCTGAATCAGAAGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAA
CGTTCTGAAGAGCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCT
GATGAATCTGAACGGTAATTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATG
CTCTTGAAAATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACG
ATGAGGTTGCACGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTG
CAGAAGCTGCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAA
GTCATTGGAAGTGTCAGAAGAGAAGGCAAATCAACGTGAAGAAGAATATAAGAATCAAAT
TAAGACTCTTACCACCCGCCTTAAGGAGAGCCGAATTTGCTGAACGTTCAGTTCAGAAAT
TGCAGAAAGAAGTCGACAGACTTGAAGATGAGCTTGTTTCCGAAAAGGAGAAATACAGAG
AAATTGGAGACGATCTCGATACCGCTTTTGTGGAACTCATCCTTAAGGAATAAAGGATTT
TCGGCCTACAAAAACATCAAAGCTTACAATGAAATGAACGTTTTACATAAATTTGAAAAA
CTCTTACTCTTCAAAATCTTTTTTCTAATTTATTAATTTTCCTTCAGTTAACGCGCATCG
ATATACATATATTGTGGATAAGATCAAAGATAGAATTAGGAAAAATTTATTCATATTAAG
CATGTAAAGTTTATCATTTAAATATTACAACCAAGATCATAAGAGATATAGAGATAAATG
TAAAACTGCAAATAACATCAATCTGAAATCTCTCACTCTTGATCGAAATTGGGGTTTAGG
AATAAAGTTAAAACGCCAACATCAGCGAACAAAATTTTTGATATATTTTTTAATTTCAAA
ATGCAAAAATAAAAAGTTTCTTTTTAGAATGTTT
>g11466.t20 Gene=g11466 Length=125
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESER
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g11466.t20 | Coils | Coil | Coil | 1 | 125 | - |
| 7 | g11466.t20 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 78 | 3.5E-29 |
| 6 | g11466.t20 | Gene3D | G3DSA:1.20.5.340 | - | 79 | 123 | 8.8E-7 |
| 5 | g11466.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 106 | 125 | - |
| 2 | g11466.t20 | PANTHER | PTHR19269:SF53 | TROPOMYOSIN-2 | 1 | 125 | 1.1E-37 |
| 3 | g11466.t20 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 125 | 1.1E-37 |
| 1 | g11466.t20 | Pfam | PF12718 | Tropomyosin like | 7 | 125 | 2.7E-26 |
| 4 | g11466.t20 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 125 | 2.51E-36 |
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. There were no conditions that were differentially expressed