General information for g11466.t63
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.t63 | isoform | g11466.t63 | 16399509 | 16404672 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon1 | 16399509 | 16399573 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS1 | 16399511 | 16399573 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon2 | 16400314 | 16400376 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS2 | 16400314 | 16400376 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon3 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS3 | 16400819 | 16400894 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon4 | 16401559 | 16401629 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS4 | 16401559 | 16401629 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon5 | 16403142 | 16403259 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS5 | 16403142 | 16403259 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon6 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS6 | 16403395 | 16403528 |
| chr_1 | g11466 | g11466.t63 | exon | g11466.t63.exon7 | 16404204 | 16404672 |
| chr_1 | g11466 | g11466.t63 | cds | g11466.t63.CDS7 | 16404204 | 16404347 |
| chr_1 | g11466 | g11466.t63 | TSS | g11466.t63 | 16404668 | 16404668 |
| chr_1 | g11466 | g11466.t63 | TTS | g11466.t63 | NA | NA |
Sequences
>g11466.t63 Gene=g11466 Length=996
AATTAGGTTTCGCCCATTTTTTTATTGATGACTTAAATCATTCCGCGAGTGAGTTTTAAG
TAAATTAAAGTGATAAATAACAAATATTAATTAATTTCAATCTTTTCCTCACTATATTTG
ATCATTAATAATTCGATTTATCTTGGTTATAGTTGTAAAATTTTCAAGTTACACTGAAAA
TTTTGTATTTTAAAAAAGAAGAAGTATTAGCAATTGAGCGAAAAAAATTTGAGTTTTGCG
GTGTGGTGTTCTAATTTTTAACTAAGTAAAAAAGAAAAAAATATTTTTTAAGTGAAATTT
AATACTAAAGAAAAAAGTTTCAACAATGACGACAAATTTGCAACAAGGCACACTCCTTGA
TGTTCTCAAGAAAAAAATGCGTCAAACAAAAGAAGAAATGGAGCGCTATAAGGATGAATG
TGAAGAATTTAATCGCAAATATCAACTTGAAGCAATGAGACGCGAAGAAGCTGAATCAGA
AGTCGCTGCTTTGAACCGTCGTATTCAACTTTTGGAAGAAGACCTCGAACGTTCTGAAGA
GCGTTTGGCATCTGCTACCGCAAAGTTGTCAGAAGCATCAGCTGCTGCTGATGAATCTGA
ACGAATAAGAAAAGCTTTGGAAAATCGCACCAATATGGAAGATGATCGAGTGGCCATCCT
AGAAGCTCAATTAACGCAGGCGAAATTAATTGCAGAAGAAGCCGATAAAAAATACGAGGA
GGTCGCCAGAAAATTAGTTTTGATGGAGCAAGATTTAGAGCGTTCCGAAGAAAAAGTTGA
ATTAAGCGAAAGCAAAATTGTTGAACTTGAAGAAGAACTTCGCGTCGTCGGTAACAACTT
GAAGTCATTGGAAGTGTCAGAAGAGAAGGCAACACAAAGGGAGGAGACGTTTGAAGGTCA
AGTGAGAATACTGGAAGGACACTTAAAGGAGGCTGAAGCCAGAGCCGAATTTGCTGAACG
TTCAGTTCAGAAATTGCAGAAAGAAGTCGACAGACT
>g11466.t63 Gene=g11466 Length=223
MTTNLQQGTLLDVLKKKMRQTKEEMERYKDECEEFNRKYQLEAMRREEAESEVAALNRRI
QLLEEDLERSEERLASATAKLSEASAAADESERIRKALENRTNMEDDRVAILEAQLTQAK
LIAEEADKKYEEVARKLVLMEQDLERSEEKVELSESKIVELEEELRVVGNNLKSLEVSEE
KATQREETFEGQVRILEGHLKEAEARAEFAERSVQKLQKEVDR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g11466.t63 | Coils | Coil | Coil | 11 | 107 | - |
| 15 | g11466.t63 | Coils | Coil | Coil | 109 | 178 | - |
| 13 | g11466.t63 | Coils | Coil | Coil | 193 | 220 | - |
| 11 | g11466.t63 | Gene3D | G3DSA:1.20.5.340 | - | 8 | 107 | 1.2E-14 |
| 12 | g11466.t63 | Gene3D | G3DSA:1.20.5.340 | - | 127 | 223 | 3.7E-17 |
| 2 | g11466.t63 | PANTHER | PTHR19269:SF45 | TROPOMYOSIN-1, ISOFORMS 33/34 | 12 | 223 | 9.1E-80 |
| 3 | g11466.t63 | PANTHER | PTHR19269 | TROPOMYOSIN | 12 | 223 | 9.1E-80 |
| 7 | g11466.t63 | PRINTS | PR00194 | Tropomyosin signature | 52 | 69 | 1.5E-53 |
| 5 | g11466.t63 | PRINTS | PR00194 | Tropomyosin signature | 88 | 108 | 1.5E-53 |
| 8 | g11466.t63 | PRINTS | PR00194 | Tropomyosin signature | 113 | 141 | 1.5E-53 |
| 6 | g11466.t63 | PRINTS | PR00194 | Tropomyosin signature | 143 | 166 | 1.5E-53 |
| 4 | g11466.t63 | PRINTS | PR00194 | Tropomyosin signature | 199 | 223 | 1.5E-53 |
| 1 | g11466.t63 | Pfam | PF00261 | Tropomyosin | 16 | 223 | 1.3E-78 |
| 10 | g11466.t63 | ProSitePatterns | PS00326 | Tropomyosins signature. | 200 | 208 | - |
| 9 | g11466.t63 | SUPERFAMILY | SSF57997 | Tropomyosin | 11 | 223 | 4.01E-62 |
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.
