General information for g11466.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t3 | TTS | g11466.t3 | 16398326 | 16398326 |
| chr_1 | g11466 | g11466.t3 | isoform | g11466.t3 | 16399209 | 16406824 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon1 | 16399209 | 16399291 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS1 | 16399209 | 16399291 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS2 | 16399504 | 16399573 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon3 | 16400314 | 16400376 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS3 | 16400314 | 16400376 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon4 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS4 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon5 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS5 | 16401901 | 16401971 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon6 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS6 | 16402845 | 16402962 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon7 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS7 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon8 | 16404204 | 16404362 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS8 | 16404204 | 16404362 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon9 | 16404974 | 16405690 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS9 | 16404974 | 16405690 |
| chr_1 | g11466 | g11466.t3 | exon | g11466.t3.exon10 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t3 | cds | g11466.t3.CDS10 | 16406585 | 16406824 |
| chr_1 | g11466 | g11466.t3 | TSS | g11466.t3 | 16407060 | 16407060 |
Sequences
>g11466.t3 Gene=g11466 Length=1731
ATGGATGCGATTAAGAAAAAAATGCAAGCAATGAAGCTTGAGAAGGATAACGCATTAGAT
CGCGCCCTTCTCTGTGAACAGCAAGCTCGTGATGCAAACACACGTGCTGAAAAGGCCGAA
GAAGAGGCCCGCACATTGCAAAAGAAGATCCAAACAATTGAAAATGATTTGGATCAGACA
CAAGAACAAGAGACTCTTGTTAATGGAAAGCTTGAAGAAAAAGAAAAGGCACTTCAAAAT
ATAGAAAAAAAATATGTGATAAAGAAATTTTCACCAAATGGCATTAACACAATGACTGAA
AGAAGTGCTCATCCGACAAATAAATCTAGGCGAGGTCATCAATATCATCCCAAAAATATA
GGCAGCAGAGGAACTTGTCGTAATGTTCCGACAAGTGAAATAATTGAAGCTCTGAGGGAG
GGCAGAAACTTGGAGTCATTATTTATACAGCATCATCAAAGTCAACATGAAAATATTCAA
TCCGATTTACCATCAGACTTAACATTATCAACATCATCAGATGCATCAAGTCAATCTGAT
CAAACTACAACATTTCACAATTTGGATTTTAATTCGAGAGAAGAATTTCAAGAAAACATT
AGCGAAGAAATTTCAATATCCAGCAACACACAAAAATATTCAAAGAGTTCAGAGCCAAAG
AGGAAGAGAAGTAAGGGTTCACAAAATGACGTACTGAGAGTTGTGCAATCAACAAGCAAT
GAAATCCTTAATAATATCAATGAAGACGATGATGCCGAAATGGTGGAGCTAGCTAAACTG
CGATGTACGAGTGAGAGAACTGAAGTTATCGCCGAACGAGAACACCGAAGACAAAAGAAG
TGTGCAGATTATCCTGGTCTTGCATTCGGACGATCGATCTTTAGCTCAGATTCAATGATG
AAATTTAATATAATTAGAAATGAATTACAAAATATCATGAATAATCAATTAAGAAGGAAA
AAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGATGTTCTCAAGAAA
AAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATGTGAAGAATTTAAT
CGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGAAGTCGCTGCTTTG
AACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGAGCGTTTGGCATCT
GCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGAACGTGCCCGTAAA
GTTCTTGAAAACCGTTCACTTGCCGATGAAGAGCGTATGGATGCTCTTGAAAATCAATTG
AAGGAAGCTCGCTTCCTCGCTGAAGAAGCTGACAAGAAATACGATGAGGTTGCACGTAAA
TTAGCTATGGTTGAGGCTGATCTTGAACGTGCAGAAGAGCGTGCAGAAGCTGGTGAAGCC
AAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTTGAAGTCATTGGAA
GTGTCAGAAGAGAAGGCAACACAAAGGGAGGAGACGTTTGAAGGTCAAGTGAGAATACTG
GAAGGACACTTAAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACGTTCAGTTCAGAAA
TTGCAGAAAGAAGTCGACAGACTTGAAGATGAATTGTTAAATGAGCGTGCACGAAACAAG
ATGCTCCAGGAAGAAATGGAAGCGACACTTCATGATATTCAGAATATGTAA
>g11466.t3 Gene=g11466 Length=576
MDAIKKKMQAMKLEKDNALDRALLCEQQARDANTRAEKAEEEARTLQKKIQTIENDLDQT
QEQETLVNGKLEEKEKALQNIEKKYVIKKFSPNGINTMTERSAHPTNKSRRGHQYHPKNI
GSRGTCRNVPTSEIIEALREGRNLESLFIQHHQSQHENIQSDLPSDLTLSTSSDASSQSD
QTTTFHNLDFNSREEFQENISEEISISSNTQKYSKSSEPKRKRSKGSQNDVLRVVQSTSN
EILNNINEDDDAEMVELAKLRCTSERTEVIAEREHRRQKKCADYPGLAFGRSIFSSDSMM
KFNIIRNELQNIMNNQLRRKKVSTMTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFN
RKYQLEAMRREEAESEVAALNRRIQLLEEDLERSEERLASATAKLSEASAAADESERARK
VLENRSLADEERMDALENQLKEARFLAEEADKKYDEVARKLAMVEADLERAEERAEAGEA
KIVELEEELRVVGNNLKSLEVSEEKATQREETFEGQVRILEGHLKEAEARAEFAERSVQK
LQKEVDRLEDELLNERARNKMLQEEMEATLHDIQNM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g11466.t3 | Coils | Coil | Coil | 1 | 63 | - |
| 17 | g11466.t3 | Coils | Coil | Coil | 335 | 502 | - |
| 18 | g11466.t3 | Coils | Coil | Coil | 517 | 576 | - |
| 14 | g11466.t3 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 81 | 6.2E-28 |
| 16 | g11466.t3 | Gene3D | G3DSA:1.20.5.340 | - | 332 | 432 | 1.7E-13 |
| 15 | g11466.t3 | Gene3D | G3DSA:1.20.5.340 | - | 452 | 551 | 2.9E-20 |
| 23 | g11466.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 99 | 128 | - |
| 22 | g11466.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 168 | 190 | - |
| 21 | g11466.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 202 | 230 | - |
| 4 | g11466.t3 | PANTHER | PTHR19269:SF45 | TROPOMYOSIN-1, ISOFORMS 33/34 | 1 | 83 | 1.4E-113 |
| 6 | g11466.t3 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 83 | 1.4E-113 |
| 3 | g11466.t3 | PANTHER | PTHR19269:SF45 | TROPOMYOSIN-1, ISOFORMS 33/34 | 336 | 573 | 1.4E-113 |
| 5 | g11466.t3 | PANTHER | PTHR19269 | TROPOMYOSIN | 336 | 573 | 1.4E-113 |
| 11 | g11466.t3 | PRINTS | PR00194 | Tropomyosin signature | 376 | 393 | 4.8E-57 |
| 7 | g11466.t3 | PRINTS | PR00194 | Tropomyosin signature | 412 | 432 | 4.8E-57 |
| 9 | g11466.t3 | PRINTS | PR00194 | Tropomyosin signature | 437 | 465 | 4.8E-57 |
| 10 | g11466.t3 | PRINTS | PR00194 | Tropomyosin signature | 467 | 490 | 4.8E-57 |
| 8 | g11466.t3 | PRINTS | PR00194 | Tropomyosin signature | 523 | 548 | 4.8E-57 |
| 1 | g11466.t3 | Pfam | PF12718 | Tropomyosin like | 7 | 82 | 1.7E-10 |
| 2 | g11466.t3 | Pfam | PF00261 | Tropomyosin | 340 | 575 | 7.4E-89 |
| 20 | g11466.t3 | ProSitePatterns | PS00326 | Tropomyosins signature. | 524 | 532 | - |
| 12 | g11466.t3 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 78 | 4.09E-21 |
| 13 | g11466.t3 | SUPERFAMILY | SSF57997 | Tropomyosin | 325 | 576 | 6.54E-75 |
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 transcript has been annotated with K09290 (tropomyosin 3)
Pathway
- This transcript belongs to the following pathways
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.
