General information for g11466.t40
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.t40 | isoform | g11466.t40 | 16397067 | 16407076 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon1 | 16397067 | 16397553 |
| chr_1 | g11466 | g11466.t40 | TTS | g11466.t40 | 16397069 | 16397069 |
| chr_1 | g11466 | g11466.t40 | cds | g11466.t40.CDS1 | 16397365 | 16397553 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t40 | cds | g11466.t40.CDS2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon3 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t40 | cds | g11466.t40.CDS3 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon4 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t40 | cds | g11466.t40.CDS4 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon5 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t40 | cds | g11466.t40.CDS5 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon6 | 16406585 | 16406868 |
| chr_1 | g11466 | g11466.t40 | cds | g11466.t40.CDS6 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t40 | exon | g11466.t40.exon7 | 16407017 | 16407076 |
| chr_1 | g11466 | g11466.t40 | TSS | g11466.t40 | 16407060 | 16407060 |
Sequences
>g11466.t40 Gene=g11466 Length=1224
AGTAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGT
TCTCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGA
AAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTG
AACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACAT
TGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTC
TTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCG
CTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTT
TGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGTG
CCCGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTTGAAA
ATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAGGTTG
CACGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTGCAGAAGCTG
GTGAAGCGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTTCAGAAATTGCAGAAAGA
AGTCGACAGACTTGAAGATGAGCTTGTTTCCGAAAAGGAGAAATACAGAGAAATTGGAGA
CGATCTCGATACCGCTTTTGTGGAACTCATCCTTAAGGAATAAAGGATTTTCGGCCTACA
AAAACATCAAAGCTTACAATGAAATGAACGTTTTACATAAATTTGAAAAACTCTTACTCT
TCAAAATCTTTTTTCTAATTTATTAATTTTCCTTCAGTTAACGCGCATCGATATACATAT
ATTGTGGATAAGATCAAAGATAGAATTAGGAAAAATTTATTCATATTAAGCATGTAAAGT
TTATCATTTAAATATTACAACCAAGATCATAAGAGATATAGAGATAAATGTAAAACTGCA
AATAACATCAATCTGAAATCTCTCACTCTTGATCGAAATTGGGGTTTAGGAATAAAGTTA
AAACGCCAACATCAGCGAACAAAATTTTTGATATATTTTTTAATTTCAAAATGCAAAAAT
AAAAAGTTTCTTTTTAGAATGTTT
>g11466.t40 Gene=g11466 Length=273
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEALKPEPNLLNVQFRNCRKKSTDLKMSLFPKRRNTEKLETISIPLLWNSSLRNK
GFSAYKNIKAYNEMNVLHKFEKLLLFKIFFLIY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11466.t40 | Coils | Coil | Coil | 1 | 189 | - |
| 9 | g11466.t40 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 95 | 7.9E-36 |
| 8 | g11466.t40 | Gene3D | G3DSA:1.20.5.340 | - | 96 | 139 | 1.4E-5 |
| 2 | g11466.t40 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 199 | 1.2E-67 |
| 4 | g11466.t40 | PRINTS | PR00194 | Tropomyosin signature | 84 | 101 | 1.0E-35 |
| 6 | g11466.t40 | PRINTS | PR00194 | Tropomyosin signature | 120 | 140 | 1.0E-35 |
| 3 | g11466.t40 | PRINTS | PR00194 | Tropomyosin signature | 145 | 173 | 1.0E-35 |
| 5 | g11466.t40 | PRINTS | PR00194 | Tropomyosin signature | 175 | 198 | 1.0E-35 |
| 1 | g11466.t40 | Pfam | PF00261 | Tropomyosin | 48 | 188 | 8.1E-50 |
| 7 | g11466.t40 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 191 | 2.04E-61 |
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