General information for g16277.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 g16277 is located on chr_4: 8948278..8950228 (+ 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 | g16277 | g16277.t1 | isoform | g16277.t1 | 8948278 | 8950228 |
| chr_4 | g16277 | g16277.t1 | exon | g16277.t1.exon1 | 8948278 | 8948397 |
| chr_4 | g16277 | g16277.t1 | cds | g16277.t1.CDS1 | 8948278 | 8948397 |
| chr_4 | g16277 | g16277.t1 | exon | g16277.t1.exon2 | 8948573 | 8949234 |
| chr_4 | g16277 | g16277.t1 | cds | g16277.t1.CDS2 | 8948573 | 8949234 |
| chr_4 | g16277 | g16277.t1 | exon | g16277.t1.exon3 | 8949304 | 8950228 |
| chr_4 | g16277 | g16277.t1 | cds | g16277.t1.CDS3 | 8949304 | 8950228 |
| chr_4 | g16277 | g16277.t1 | TTS | g16277.t1 | 8950657 | 8950657 |
| chr_4 | g16277 | g16277.t1 | TSS | g16277.t1 | NA | NA |
Sequences
>g16277.t1 Gene=g16277 Length=1707
ATGTTTAAAAATTTATTTATTTTAAAGCCTAAAATTCAATTGAAATTTGTTAAAAATTTT
CATATCAATGACACAAATATCATAAAAACAAAAGTTGATAGAAATTCATCAGAATTTAAG
GAAAATTTTGCCTCACTTCAATCACTTGTAGATGAACTCAATGAAATTACTCAAAAAACT
CTCACACCTGATCTAGCAGCCATCAAGAAAAGCCAAGCAAGCAAAAAGCTCCTCGTTCGT
GATCGAGTCAATCGTCTTCTCGATCCAGGCACAGCATTTCTTGAACTTTCTCAACTTGCA
GCTTACAATCTTTATGGAAAAGAAGACATAAAGTCAGCTGGATTTATAACTGGCATTGGA
AAAGTATGTGGTCAACTTACAATGATAACTGCAAATGATTCTTCAATTAAAGGCGGTTCA
ATGTATCCAGTCACAGTCAAAAAGCATTTAAGAGCTCAAGAAATTGCTCAAGAAAATCGA
CTGCCATGCATTTATTTAGTTGATTCTGCAGGAGCAAATTTAATGCGTCAAGCTGAATTT
TTTGTCGAAGGTGGACGAATTTTTTATAATCAAGCTGTGATGTCATCAATGGGAATTCCT
CAAGTTGTTGTTGTTATGGGAAGTTGTACAGCTGGCGGTGCTTATGTGCCGACAATGTCT
GATGAAAATATTATTGTGAAAGAACAAGGAACACTTTTCCTTGGTGGTCCACCTTTAGTT
AAAGCTGCATTAGGTGAAATTGTAACAGCTGAAGAATTAGGTGGTGCTGACTTGCATTGC
AGAGTCTCAGGATGTTCAGATCATTATGCTCTTGATGATGAGCATGCTCTTTATATGGCA
AGACAAATTATGGCAAATTTAAATAAAAAAACAACAAATAATTACAATGATAACTTAAAA
TTCAACTATCGACTTAAAGAACCTTCAGTTGAAATTGAAGAACCACTTTATGATCCAACA
GAACTTTATGGAATTGTCAATTCGTCATTAACTAAAAATTTTGACATTCGTGAAGTAATT
GCAAGAATTGTTGATGGTTCAAAATTCCAAGAATTTAAGAAATTTTATGGTGATACTTTA
GTTTGTGGTTTTGCAAAGCTTTATGGAACGACAATTGGAATTGTTGGCAATAATGGTGTT
CTTTTTAGTGAGTCAGCACTTAAAGGAGCTCACTTTATTCAACTCTGTTCACAACGTGGA
ATTCCCTTGCTTTTTCTTCAAAATATCACTGGTTTTATGGTCGGACGTGAAGCAGAATCA
CAAGGGATTGCAAAGAATGGAGCTAAAATGGTCAATGCTGTTGCAACAGCTCGTGTGCCA
AAGTTGACTGTTATTGTTGGTGGCTCTTATGGTGCTGGTAATTATGGAATGTGTGGACGA
GCTTACAGCCCGAGATTCCTTTATATGTGGCCAAATTCAAGAATTTCAGTAATGGGTGGA
GCTCAAGCAGCTGGTGTAATTGCACAAATAACCAAAGATCAATTTAAAAGATCAGGCAAG
GAATGGACAAAAGAAATTGAAGATAAAATTAAAGAACCTTTGATAAAGCAATTTGAGGCA
GAAAGTTCAGCTTATTACAGTACAGCAAGATTATGGGATGATGGAATTATTGATCCAAAA
GACACAAGAAAGGTTTTAGGTTTATCATTGGCTGCTGCTTTGAATGCTCCAATTGAGGAA
AGCAAACATGGAGTTTTTAGAATGTAA
>g16277.t1 Gene=g16277 Length=568
MFKNLFILKPKIQLKFVKNFHINDTNIIKTKVDRNSSEFKENFASLQSLVDELNEITQKT
LTPDLAAIKKSQASKKLLVRDRVNRLLDPGTAFLELSQLAAYNLYGKEDIKSAGFITGIG
KVCGQLTMITANDSSIKGGSMYPVTVKKHLRAQEIAQENRLPCIYLVDSAGANLMRQAEF
FVEGGRIFYNQAVMSSMGIPQVVVVMGSCTAGGAYVPTMSDENIIVKEQGTLFLGGPPLV
KAALGEIVTAEELGGADLHCRVSGCSDHYALDDEHALYMARQIMANLNKKTTNNYNDNLK
FNYRLKEPSVEIEEPLYDPTELYGIVNSSLTKNFDIREVIARIVDGSKFQEFKKFYGDTL
VCGFAKLYGTTIGIVGNNGVLFSESALKGAHFIQLCSQRGIPLLFLQNITGFMVGREAES
QGIAKNGAKMVNAVATARVPKLTVIVGGSYGAGNYGMCGRAYSPRFLYMWPNSRISVMGG
AQAAGVIAQITKDQFKRSGKEWTKEIEDKIKEPLIKQFEAESSAYYSTARLWDDGIIDPK
DTRKVLGLSLAAALNAPIEESKHGVFRM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16277.t1 | Gene3D | G3DSA:3.90.226.10 | - | 25 | 292 | 0.000 |
| 6 | g16277.t1 | Gene3D | G3DSA:3.90.226.10 | - | 306 | 568 | 0.000 |
| 2 | g16277.t1 | PANTHER | PTHR22855 | ACETYL, PROPIONYL, PYRUVATE, AND GLUTACONYL CARBOXYLASE-RELATED | 21 | 568 | 0.000 |
| 1 | g16277.t1 | Pfam | PF01039 | Carboxyl transferase domain | 75 | 563 | 0.000 |
| 8 | g16277.t1 | ProSiteProfiles | PS50980 | Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. | 46 | 299 | 45.949 |
| 7 | g16277.t1 | ProSiteProfiles | PS50989 | Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. | 311 | 560 | 50.054 |
| 3 | g16277.t1 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 57 | 292 | 0.000 |
| 4 | g16277.t1 | SUPERFAMILY | SSF52096 | ClpP/crotonase | 309 | 568 | 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 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.
