General information for g15546.t1
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.t1 | TTS | g15546.t1 | 5808879 | 5808879 |
| chr_4 | g15546 | g15546.t1 | isoform | g15546.t1 | 5809242 | 5811083 |
| chr_4 | g15546 | g15546.t1 | exon | g15546.t1.exon1 | 5809242 | 5810166 |
| chr_4 | g15546 | g15546.t1 | cds | g15546.t1.CDS1 | 5809242 | 5810166 |
| chr_4 | g15546 | g15546.t1 | exon | g15546.t1.exon2 | 5810232 | 5810902 |
| chr_4 | g15546 | g15546.t1 | cds | g15546.t1.CDS2 | 5810232 | 5810902 |
| chr_4 | g15546 | g15546.t1 | exon | g15546.t1.exon3 | 5810967 | 5811083 |
| chr_4 | g15546 | g15546.t1 | cds | g15546.t1.CDS3 | 5810967 | 5811083 |
| chr_4 | g15546 | g15546.t1 | TSS | g15546.t1 | 5811141 | 5811141 |
Sequences
>g15546.t1 Gene=g15546 Length=1713
ATGCTCAATCTAAAGCGACAAACATTAAATTTGACACTTCGACATGTTCGGCAACTTCAC
ATGTTTGAAGCAAATGTCATCACATCAAAAATCGACAAAAATTCAACTGAATATCAGGAA
AATTTTAATTCCCTTAAAGCCATGGTCAATAATTTGCAGCTAATTACACAGAATGTGCTA
AGAACTGATGAGACAGCAATCAAGAGACATCAATCAAAAAATAAATTACTCGTTCGTGAT
CGAATCAACAAGTTGCTGGATCCAAATTCAGCATTTCTCGAATTGTCACAACTTGCTGGT
TATGAGCTCTATGGTAAAGAGCAAGTAAATTCTGCTGGGATTGTGACTGGCATTGGAAAA
GTGAGTGGTCAACTAGCAATGATTGTTGGCAATGATGCGACAGTCAAAGGTGGAACTTAC
TATCCAATTACAGTTAAAAAACATCTTAGAGCTCAAGAAATTGCTCAAGAAAATCGATTG
CCTTGCATTTATCTAGTCGATTCAGGCGGTGCAAATTTACCACGACAAGCTGAAGTTTTT
CCTGACAAACAACATTTTGGTAGAATTTTCTTTAATCAAGCAAACATGTCAGCATTAAAT
ATTCCACAAATTGCTGTTGTTATGGGCAGTTGCACTGCTGGTGGAGCTTACGTTCCTGCT
ATGGCTGATGAATCAATTATTGTGAAACAACAAGGAACAATTTTCCTTGCTGGCCCGCCA
CTTGTTAAAGCAGCAACAGGTGAAGAAGTTTCAGCTGAAGATCTTGGTGGTGCTGATTTA
CATTGCAGAACATCTGGTGTGACTGATCATTATGCACTCGATGATGAACATGCTCTTTAT
TTGGCACGTCAAGTTGTGGCCAATTTAAATCTTCCAGCAACAAATAATTACAATGAATTA
CTTAGTTTAAATTATAGAAATCAAACACCAATGACCAATATTGAAGAACCACTTTATGAT
CCAACAGAACTTTATGGAATTGTTAATTCATCATTAACTAAAAATTTTGACATTCGTGAA
GTAATTGCAAGAATTGTTGATGGTTCGAGATTTCAAGAATTTAAGAAATTTTATGGTGAC
ACTTTAGTTTGTGGTTTTGCAAAGCTTTATGGAACAACAATTGGAATTGTTGGCAATAAT
GGTGTTCTTTTTAGTGAGTCAGCACTTAAAGGAGCTCACTTTATTCAATTATGCTCACAA
CGTGGAATTCCTTTGCTTTTCCTTCAAAATATCACTGGTTTTATGGTTGGACGTGAAGCA
GAATCACAAGGAATTGCAAAGAATGGAGCTAAAATGGTCAATGCTGTTGCAACAGCTCGT
GTGCCAAAGTTAACTGTTATTGTTGGTGGTTCTTATGGTGCTGGTAATTATGGCATGTGT
GGACGAGCCTACAGCCCGAGATTCCTTTATATGTGGCCAAATTCAAGAATTTCAGTAATG
GGAGGAGCTCAAGCAGCTGGAGTGATTGCTCAAATTACTGAAGATCAATACAAAAGATCA
GGCAAGGAATGGACACAAGAAATTGGTGATAAAATAAAAGCACCATTAATTAAACAATTT
GAGGCAGAAAGTTCAGCTTATTACAGTACAGCAAGATTATGGGATGATGGAATTATCGAT
CCTGTTGATACAAGAAGAGTTTTAGGTTTATCATTGGCTGCAGCATTAAATGCTCCAATT
GAAGAGACTAAACATGGTGTGTTTAGAATGTAA
>g15546.t1 Gene=g15546 Length=570
MLNLKRQTLNLTLRHVRQLHMFEANVITSKIDKNSTEYQENFNSLKAMVNNLQLITQNVL
RTDETAIKRHQSKNKLLVRDRINKLLDPNSAFLELSQLAGYELYGKEQVNSAGIVTGIGK
VSGQLAMIVGNDATVKGGTYYPITVKKHLRAQEIAQENRLPCIYLVDSGGANLPRQAEVF
PDKQHFGRIFFNQANMSALNIPQIAVVMGSCTAGGAYVPAMADESIIVKQQGTIFLAGPP
LVKAATGEEVSAEDLGGADLHCRTSGVTDHYALDDEHALYLARQVVANLNLPATNNYNEL
LSLNYRNQTPMTNIEEPLYDPTELYGIVNSSLTKNFDIREVIARIVDGSRFQEFKKFYGD
TLVCGFAKLYGTTIGIVGNNGVLFSESALKGAHFIQLCSQRGIPLLFLQNITGFMVGREA
ESQGIAKNGAKMVNAVATARVPKLTVIVGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVM
GGAQAAGVIAQITEDQYKRSGKEWTQEIGDKIKAPLIKQFEAESSAYYSTARLWDDGIID
PVDTRRVLGLSLAAALNAPIEETKHGVFRM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g15546.t1 | Gene3D | G3DSA:3.90.226.10 | - | 24 | 293 | 0.000 |
| 7 | g15546.t1 | Gene3D | G3DSA:3.90.226.10 | - | 308 | 570 | 0.000 |
| 2 | g15546.t1 | PANTHER | PTHR22855 | ACETYL, PROPIONYL, PYRUVATE, AND GLUTACONYL CARBOXYLASE-RELATED | 30 | 570 | 0.000 |
| 3 | g15546.t1 | PANTHER | PTHR22855:SF13 | METHYLCROTONOYL-COA CARBOXYLASE BETA CHAIN, MITOCHONDRIAL | 30 | 570 | 0.000 |
| 1 | g15546.t1 | Pfam | PF01039 | Carboxyl transferase domain | 70 | 566 | 0.000 |
| 9 | g15546.t1 | ProSiteProfiles | PS50980 | Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. | 44 | 301 | 55.272 |
| 8 | g15546.t1 | ProSiteProfiles | PS50989 | Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. | 313 | 562 | 50.705 |
| 5 | g15546.t1 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 56 | 292 | 0.000 |
| 4 | g15546.t1 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 313 | 570 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016874 | ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01969 (3-methylcrotonyl-CoA carboxylase beta subunit)
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.
