General information for g11466.t39
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.t39 | isoform | g11466.t39 | 16397067 | 16407076 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon1 | 16397067 | 16397553 |
| chr_1 | g11466 | g11466.t39 | TTS | g11466.t39 | 16397069 | 16397069 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon3 | 16400629 | 16400691 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon4 | 16401882 | 16401971 |
| chr_1 | g11466 | g11466.t39 | cds | g11466.t39.CDS1 | 16401897 | 16401971 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon5 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t39 | cds | g11466.t39.CDS2 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon6 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t39 | cds | g11466.t39.CDS3 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon7 | 16406585 | 16406868 |
| chr_1 | g11466 | g11466.t39 | cds | g11466.t39.CDS4 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t39 | exon | g11466.t39.exon8 | 16407017 | 16407076 |
| chr_1 | g11466 | g11466.t39 | TSS | g11466.t39 | 16407060 | 16407060 |
Sequences
>g11466.t39 Gene=g11466 Length=1306
AGTAAAGTTTTTCTTCAGTTCGCCATCAAAACTGTTCAAGTCGCGGATTCAGATTCAAGT
TCTCTGGTGCTTTCGTAATACCGTAGTAAAAACACATTACCAAAATGGATGCGATTAAGA
AAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGATCGCGCCCTTCTCTGTG
AACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAAGAAGAGGCCCGCACAT
TGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACACAAGAACAAGAGACTC
TTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAATGCTGAATCAGAAGTCG
CTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTT
TGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGTG
CCCGTAAAGTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTTGAAA
ATCAATTGAAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAGGTTG
CACGTAAATTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTGCAGAAGCTG
GTGAAGCGTAAGAGTCTTCATGAATTGCAAATCAACGTGAAGAAGAATATAAGAATCAAA
TTAAGACTCTTACCACCCGCCTTAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACGTT
CAGTTCAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGATGAGCTTGTTTCCGAAAAGG
AGAAATACAGAGAAATTGGAGACGATCTCGATACCGCTTTTGTGGAACTCATCCTTAAGG
AATAAAGGATTTTCGGCCTACAAAAACATCAAAGCTTACAATGAAATGAACGTTTTACAT
AAATTTGAAAAACTCTTACTCTTCAAAATCTTTTTTCTAATTTATTAATTTTCCTTCAGT
TAACGCGCATCGATATACATATATTGTGGATAAGATCAAAGATAGAATTAGGAAAAATTT
ATTCATATTAAGCATGTAAAGTTTATCATTTAAATATTACAACCAAGATCATAAGAGATA
TAGAGATAAATGTAAAACTGCAAATAACATCAATCTGAAATCTCTCACTCTTGATCGAAA
TTGGGGTTTAGGAATAAAGTTAAAACGCCAACATCAGCGAACAAAATTTTTGATATATTT
TTTAATTTCAAAATGCAAAAATAAAAAGTTTCTTTTTAGAATGTTT
>g11466.t39 Gene=g11466 Length=188
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11466.t39 | Coils | Coil | Coil | 1 | 188 | - |
| 11 | g11466.t39 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 96 | 3.2E-36 |
| 10 | g11466.t39 | Gene3D | G3DSA:1.20.5.340 | - | 97 | 139 | 1.4E-5 |
| 8 | g11466.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 106 | 136 | - |
| 9 | g11466.t39 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 136 | - |
| 2 | g11466.t39 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 188 | 6.6E-68 |
| 4 | g11466.t39 | PRINTS | PR00194 | Tropomyosin signature | 84 | 101 | 7.7E-39 |
| 5 | g11466.t39 | PRINTS | PR00194 | Tropomyosin signature | 120 | 140 | 7.7E-39 |
| 3 | g11466.t39 | PRINTS | PR00194 | Tropomyosin signature | 145 | 173 | 7.7E-39 |
| 6 | g11466.t39 | PRINTS | PR00194 | Tropomyosin signature | 175 | 188 | 7.7E-39 |
| 1 | g11466.t39 | Pfam | PF00261 | Tropomyosin | 48 | 187 | 4.7E-50 |
| 7 | g11466.t39 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 187 | 1.47E-60 |
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.
