General information for g11464.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tropomyosin-1.
Parent gene
- The parent gene g11464 is located on chr_1: 16393544..16395040 (- 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 | g11464 | g11464.t20 | isoform | g11464.t20 | 16389951 | 16395040 |
| chr_1 | g11464 | g11464.t20 | exon | g11464.t20.exon1 | 16389951 | 16390388 |
| chr_1 | g11464 | g11464.t20 | TTS | g11464.t20 | 16389991 | 16389991 |
| chr_1 | g11464 | g11464.t20 | cds | g11464.t20.CDS1 | 16390306 | 16390388 |
| chr_1 | g11464 | g11464.t20 | exon | g11464.t20.exon2 | 16393192 | 16393369 |
| chr_1 | g11464 | g11464.t20 | cds | g11464.t20.CDS2 | 16393192 | 16393369 |
| chr_1 | g11464 | g11464.t20 | exon | g11464.t20.exon3 | 16393544 | 16393763 |
| chr_1 | g11464 | g11464.t20 | cds | g11464.t20.CDS3 | 16393544 | 16393763 |
| chr_1 | g11464 | g11464.t20 | exon | g11464.t20.exon4 | 16393833 | 16394191 |
| chr_1 | g11464 | g11464.t20 | cds | g11464.t20.CDS4 | 16393833 | 16394185 |
| chr_1 | g11464 | g11464.t20 | exon | g11464.t20.exon5 | 16394969 | 16395040 |
| chr_1 | g11464 | g11464.t20 | TSS | g11464.t20 | 16395053 | 16395053 |
Sequences
>g11464.t20 Gene=g11464 Length=1267
ATTTTGTGTTGCGAGGATCTTTATAGAGCGCTCAGGTCAGTTTTTTATTAGGAGAGAGCA
AAAATATTTATGAAGAAGATGCAAGCAATGAAGCTTGAGAAAGATAATGCTCAAGACAAA
GCTGACACCTGCGAGAATCAAGCCAAGGATGCCAACGCCAAGGCCGCTAAGGTCGAAGAA
GAAGTTGCCGATTTGATCAAGAAATTGGCTCAAGTTGAAAGCGATTTGGAAGCACACAAG
AATGCTTTGGAGCAAGCCAACAAGGATTTAGAAGAAAAAGAAAAGCTCCTCACAACCACA
GAATCAGAAGTTGCTGCATTAAACAGAAAAGTACAACAGGTTGAAGAAGATTTGGAAAAG
TCAGAAGAACGCTCATCAACTGCTATGCAAAAACTTTTGGAAGCCACACAAGCTGCTGAT
GAAAATAACCGTATGTGCAAGGTATTGGAGAATCGTGCACAGCAAGATGAAGAGCGCATG
GATCAATTGACAAACCAACTTAAAGAAGCACGTCTCCTTGCTGAAGACGCCGATGGTAAA
TCAGATGAAGTTTCACGCAAGTTGGCCTTCGTTGAAGATGAATTGGAAGTTGCTGAAGAT
CGTGTTAAGTCAGGAGAGGCAAAGATCATGGAACTTGAAGAAGAATTGAAGGTTGTTGGT
AACTCATTGAAATCATTGGAAGTATCAGAAGAAAAGGCTAACCAGAGAGTTGAAGAATTC
AAACGTCAATTGAAATCATTGACAATCAAACTTAAGGAAGCCGAAAATCGTGCAGAATTG
GCTGAGAAGACAGTCAAGAAACTGCAAAAGGAAGTTGACAGACTTGAAGATGAACTTGGT
CTCAACAAAGACAGATACAAGTCACTTGCCGATGAAATGGATTCAACCTTTGCTGAATTG
GCAGGCTATTAAACAATCACCATTGTGTGTGAAATCGAAGCAAAGCGAAAACTGTGCATG
TCTTGAAGAACGTTCTGTAAACAATAACTATTTATTTAAATCACATAAACATGATGTATC
TCTTTTTTTTTGCTATTCAGATCGAATAACTTTTTTTTGTCCAACACGAGAAAGTTACTT
TTAGAAATCTCATAATGTCTTATTTTACAATACAATAATTGAAAAAGTATCAAAAGTTCT
AACATTTTTTATTGTTTTATGATGGAAAGAAAATTTTTGTGCTCTCTCTCTTTTAAAAAA
CAGAAATCTTAATAAAGAAACTGTAACAAAAAAATCTTATGATGATAGATAGAATTTATA
GGAAAAT
>g11464.t20 Gene=g11464 Length=277
MQAMKLEKDNAQDKADTCENQAKDANAKAAKVEEEVADLIKKLAQVESDLEAHKNALEQA
NKDLEEKEKLLTTTESEVAALNRKVQQVEEDLEKSEERSSTAMQKLLEATQAADENNRMC
KVLENRAQQDEERMDQLTNQLKEARLLAEDADGKSDEVSRKLAFVEDELEVAEDRVKSGE
AKIMELEEELKVVGNSLKSLEVSEEKANQRVEEFKRQLKSLTIKLKEAENRAELAEKTVK
KLQKEVDRLEDELGLNKDRYKSLADEMDSTFAELAGY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g11464.t20 | Coils | Coil | Coil | 1 | 105 | - |
| 13 | g11464.t20 | Coils | Coil | Coil | 113 | 266 | - |
| 11 | g11464.t20 | Gene3D | G3DSA:1.20.5.340 | - | 1 | 72 | 2.1E-18 |
| 12 | g11464.t20 | Gene3D | G3DSA:1.20.5.340 | - | 73 | 133 | 1.4E-8 |
| 10 | g11464.t20 | Gene3D | G3DSA:1.20.5.340 | - | 152 | 252 | 2.1E-18 |
| 16 | g11464.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 2 | g11464.t20 | PANTHER | PTHR19269:SF53 | TROPOMYOSIN-2 | 1 | 277 | 2.8E-149 |
| 3 | g11464.t20 | PANTHER | PTHR19269 | TROPOMYOSIN | 1 | 277 | 2.8E-149 |
| 7 | g11464.t20 | PRINTS | PR00194 | Tropomyosin signature | 77 | 94 | 6.7E-47 |
| 4 | g11464.t20 | PRINTS | PR00194 | Tropomyosin signature | 113 | 133 | 6.7E-47 |
| 8 | g11464.t20 | PRINTS | PR00194 | Tropomyosin signature | 138 | 166 | 6.7E-47 |
| 6 | g11464.t20 | PRINTS | PR00194 | Tropomyosin signature | 168 | 191 | 6.7E-47 |
| 5 | g11464.t20 | PRINTS | PR00194 | Tropomyosin signature | 224 | 249 | 6.7E-47 |
| 1 | g11464.t20 | Pfam | PF00261 | Tropomyosin | 41 | 275 | 5.4E-76 |
| 15 | g11464.t20 | ProSitePatterns | PS00326 | Tropomyosins signature. | 225 | 233 | - |
| 9 | g11464.t20 | SUPERFAMILY | SSF57997 | Tropomyosin | 1 | 276 | 2.29E-81 |
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 K10374 (tropomyosin 2)
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. There were no conditions that were differentially expressed