General information for g15546.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable methylcrotonoyl-CoA carboxylase beta chain, mitochondrial.
Parent gene
- The parent gene g15546 is located on chr_4: 5810163..5811083 (- 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_4 | g15546 | g15546.t3 | isoform | g15546.t3 | 5810163 | 5811083 |
| chr_4 | g15546 | g15546.t3 | exon | g15546.t3.exon1 | 5810163 | 5810166 |
| chr_4 | g15546 | g15546.t3 | cds | g15546.t3.CDS1 | 5810163 | 5810166 |
| chr_4 | g15546 | g15546.t3 | exon | g15546.t3.exon2 | 5810232 | 5811083 |
| chr_4 | g15546 | g15546.t3 | cds | g15546.t3.CDS2 | 5810232 | 5810878 |
| chr_4 | g15546 | g15546.t3 | TSS | g15546.t3 | 5811141 | 5811141 |
| chr_4 | g15546 | g15546.t3 | TTS | g15546.t3 | NA | NA |
Sequences
>g15546.t3 Gene=g15546 Length=856
ATGCTCAATCTAAAGCGACAAACATTAAATTTGACACTTCGACATGTTCGGCAACTTCAC
ATGTTTGAAGCAAATGTCATCACATCAAAAATCGACAAAAATTCAACTGAATATCAGGTC
TGGAAAGTCCACAGAAAATTTTTTTTATTATGACATCAAAAAAGTCTTATCTTATTTTTA
GGAAAATTTTAATTCCCTTAAAGCCATGGTCAATAATTTGCAGCTAATTACACAGAATGT
GCTAAGAACTGATGAGACAGCAATCAAGAGACATCAATCAAAAAATAAATTACTCGTTCG
TGATCGAATCAACAAGTTGCTGGATCCAAATTCAGCATTTCTCGAATTGTCACAACTTGC
TGGTTATGAGCTCTATGGTAAAGAGCAAGTAAATTCTGCTGGGATTGTGACTGGCATTGG
AAAAGTGAGTGGTCAACTAGCAATGATTGTTGGCAATGATGCGACAGTCAAAGGTGGAAC
TTACTATCCAATTACAGTTAAAAAACATCTTAGAGCTCAAGAAATTGCTCAAGAAAATCG
ATTGCCTTGCATTTATCTAGTCGATTCAGGCGGTGCAAATTTACCACGACAAGCTGAAGT
TTTTCCTGACAAACAACATTTTGGTAGAATTTTCTTTAATCAAGCAAACATGTCAGCATT
AAATATTCCACAAATTGCTGTTGTTATGGGCAGTTGCACTGCTGGTGGAGCTTACGTTCC
TGCTATGGCTGATGAATCAATTATTGTGAAACAACAAGGAACAATTTTCCTTGCTGGCCC
GCCACTTGTTAAAGCAGCAACAGGTGAAGAAGTTTCAGCTGAAGATCTTGGTGGTGCTGA
TTTACATTGCAGAACA
>g15546.t3 Gene=g15546 Length=217
MVNNLQLITQNVLRTDETAIKRHQSKNKLLVRDRINKLLDPNSAFLELSQLAGYELYGKE
QVNSAGIVTGIGKVSGQLAMIVGNDATVKGGTYYPITVKKHLRAQEIAQENRLPCIYLVD
SGGANLPRQAEVFPDKQHFGRIFFNQANMSALNIPQIAVVMGSCTAGGAYVPAMADESII
VKQQGTIFLAGPPLVKAATGEEVSAEDLGGADLHCRT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g15546.t3 | Gene3D | G3DSA:3.90.226.10 | - | 5 | 217 | 0.000 |
| 2 | g15546.t3 | PANTHER | PTHR22855 | ACETYL, PROPIONYL, PYRUVATE, AND GLUTACONYL CARBOXYLASE-RELATED | 10 | 216 | 0.000 |
| 1 | g15546.t3 | Pfam | PF01039 | Carboxyl transferase domain | 23 | 216 | 0.000 |
| 5 | g15546.t3 | ProSiteProfiles | PS50980 | Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. | 1 | 217 | 54.742 |
| 3 | g15546.t3 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 9 | 216 | 0.000 |
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.
