General information for g11466.t29
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.t29 | isoform | g11466.t29 | 16397067 | 16407046 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon1 | 16397067 | 16397553 |
| chr_1 | g11466 | g11466.t29 | TTS | g11466.t29 | 16397069 | 16397069 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon2 | 16399504 | 16399562 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS1 | 16399548 | 16399562 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon3 | 16400629 | 16400691 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS2 | 16400629 | 16400691 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon4 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS3 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon5 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS4 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon6 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS5 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon7 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS6 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon8 | 16406585 | 16406868 |
| chr_1 | g11466 | g11466.t29 | cds | g11466.t29.CDS7 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t29 | exon | g11466.t29.exon9 | 16407017 | 16407046 |
| chr_1 | g11466 | g11466.t29 | TSS | g11466.t29 | 16407060 | 16407060 |
Sequences
>g11466.t29 Gene=g11466 Length=1322
ACTGTTCAAGTCGCGGATTCAGATTCAAGTTCTCTGGTGCTTTCGTAATACCGTAGTAAA
AACACATTACCAAAATGGATGCGATTAAGAAAAAAATGCAAGCAATGAAGCTTGAGAAGG
ATAACGCATTAGATCGCGCCCTTCTCTGTGAACAGCAAGCTCGTGATGCAAACACACGTG
CTGAAAAGGCCGAAGAAGAGGCCCGCACATTGCAAAAGAAGATCCAAACAATTGAAAATG
ATTTGGATCAGACACAAGAACAAGAGACTCTTGTTAATGGAAAGCTTGAAGAAAAAGAAA
AGGCACTTCAAAATGCTGAATCAGAAGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGG
AAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAG
CATCAGCTGCTGCTGATGAATCTGAACGTGCCCGTAAAGTTCTTGAAAACCGTTCACTTG
CCGATGAAGAGCGTATGGATGCTCTTGAAAATCAATTGAAGGAAGCTCGCTTCCTCGCTG
AAGAAGCTGACAAGAAATACGATGAGGTTGCACGTAAATTAGCTATGGTTGAGGCTGATC
TTGAACGTGCAGAAGAGCGTGCAGAAGCTGGTGAAGCCAAAATTGTTGAACTTGAAGAAG
AACTTCGCGTCGTCGGTAACAACTTGAAGTCATTGGAAGTGTCAGAAGAGAAGGCAAATC
AACGTGAAGAAGAATATAAGAATCAAATTAAGACTCTTACCACCCGCCTTAAGGAGAGCC
GAATTTGCTGAACGTTCAGTTCAGAAATTGCAGAAAGAAGTCGACAGACTTGAAGATGAG
CTTGTTTCCGAAAAGGAGAAATACAGAGAAATTGGAGACGATCTCGATACCGCTTTTGTG
GAACTCATCCTTAAGGAATAAAGGATTTTCGGCCTACAAAAACATCAAAGCTTACAATGA
AATGAACGTTTTACATAAATTTGAAAAACTCTTACTCTTCAAAATCTTTTTTCTAATTTA
TTAATTTTCCTTCAGTTAACGCGCATCGATATACATATATTGTGGATAAGATCAAAGATA
GAATTAGGAAAAATTTATTCATATTAAGCATGTAAAGTTTATCATTTAAATATTACAACC
AAGATCATAAGAGATATAGAGATAAATGTAAAACTGCAAATAACATCAATCTGAAATCTC
TCACTCTTGATCGAAATTGGGGTTTAGGAATAAAGTTAAAACGCCAACATCAGCGAACAA
AATTTTTGATATATTTTTTAATTTCAAAATGCAAAAATAAAAAGTTTCTTTTTAGAATGT
TT
>g11466.t29 Gene=g11466 Length=238
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAA
DESERARKVLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAE
ERAEAGEAKIVELEEELRVVGNNLKSLEVSEEKANQREEEYKNQIKTLTTRLKESRIC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11466.t29 | Coils | Coil | Coil | 1 | 231 | - |
| 10 | g11466.t29 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 95 | 6.0E-36 |
| 9 | g11466.t29 | Gene3D | G3DSA:1.20.5.340 | - | 96 | 139 | 1.0E-5 |
| 11 | g11466.t29 | Gene3D | G3DSA:1.20.5.340 | - | 159 | 237 | 1.0E-13 |
| 8 | g11466.t29 | MobiDBLite | mobidb-lite | consensus disorder prediction | 105 | 126 | - |
| 2 | g11466.t29 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 235 | 5.6E-95 |
| 4 | g11466.t29 | PRINTS | PR00194 | Tropomyosin signature | 84 | 101 | 2.4E-44 |
| 6 | g11466.t29 | PRINTS | PR00194 | Tropomyosin signature | 120 | 140 | 2.4E-44 |
| 3 | g11466.t29 | PRINTS | PR00194 | Tropomyosin signature | 145 | 173 | 2.4E-44 |
| 5 | g11466.t29 | PRINTS | PR00194 | Tropomyosin signature | 175 | 198 | 2.4E-44 |
| 1 | g11466.t29 | Pfam | PF00261 | Tropomyosin | 48 | 235 | 8.1E-73 |
| 7 | g11466.t29 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 235 | 2.86E-78 |
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