General information for g13674.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial.
Parent gene
- The parent gene g13674 is located on chr_1: 31500776..31502322 (+ 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 | g13674 | g13674.t1 | TSS | g13674.t1 | 31498318 | 31498318 |
| chr_1 | g13674 | g13674.t1 | isoform | g13674.t1 | 31498550 | 31500776 |
| chr_1 | g13674 | g13674.t1 | exon | g13674.t1.exon1 | 31498550 | 31498566 |
| chr_1 | g13674 | g13674.t1 | cds | g13674.t1.CDS1 | 31498550 | 31498566 |
| chr_1 | g13674 | g13674.t1 | exon | g13674.t1.exon2 | 31498625 | 31499073 |
| chr_1 | g13674 | g13674.t1 | cds | g13674.t1.CDS2 | 31498625 | 31499073 |
| chr_1 | g13674 | g13674.t1 | exon | g13674.t1.exon3 | 31499134 | 31500776 |
| chr_1 | g13674 | g13674.t1 | cds | g13674.t1.CDS3 | 31499134 | 31500776 |
| chr_1 | g13674 | g13674.t1 | TTS | g13674.t1 | 31500972 | 31500972 |
Sequences
>g13674.t1 Gene=g13674 Length=2109
ATGTTATCTAGAGCGAAACTTTTTACAAAATTAAATCATCATGCTTTTATGCGATCATTC
ACAGTAAAAACAAAACCCGAAATAAAACCAATAAATAAAGTTTTAATTGCGAATAGAGGA
GAAATTGCAGTGCGTGTGATTAAAACATGCAAGAAACTTGGTATTCGAACAGTTGCAGTT
TTTTCTGATGCTGATGCAAAATCATTGCATGTGTCTATGGCTGATGAAGCATATCATATT
GGTCCAGCACTTTCATCAAAAAGTTACTTGAGGGGTGATAAAATCATTGATGTTGCACAT
TTGACTGGTGCTCAAGCCATTCATCCTGGTTATGGCTTTCTATCAGAAAGTGTAGAATTT
TCAGCATTATGTGAGAAAACAGGTGTAATTTTTATTGGCCCACCTGAGAGTGCGATTAGA
GATATGGGAATTAAAAGTACATCAAAACATATCATGACATCTGCTGGTGTTCCATGTATA
ATGGGCTATCACGGCGAAAATCAATCAGATGATTTTTTAGTAAAAGAGGCTGAGAAAATT
GGTTATCCTTTAATGATTAAAGCAGTAAGAGGTGGAGGTGGCAAAGGCATGAGAATTGCA
AACACTCCAGAGGAATTTTTGCCTCAACTTCAAAGTGCTCGAACAGAATCAGAAAAAGCA
TTTGGTGATAGCACAATGTTGCTTGAAAAATATGTTCGCAGTCCTCGTCATGTTGAAGTT
CAAGTTTTTGCTGACAAATATGGTGATGCTGTCTATTTATGGGAAAGAGATTGCTCAGTA
CAACGAAGACATCAAAAAATTATTGAAGAAGCTCCTGCACCAGGAATATCAGAAGAATTG
AGAAGAAAATTGGGTGAAGCAGCTGTGAGAGCAGCAAAAGCTGTTAATTATGTTGGCGCA
GGAACAGTTGAATTTATTTTAGATAAAGAAGATTTATCATTCCATTTTATGGAAATGAAT
ACAAGATTGCAAGTTGAGCATCCTATTACAGAAATGATTACAGGAATTGATTTAGTTGAT
TGGCAAATAAGAATTGCAAGTGGTGAACCATTGCCATTAACTCAAGAACAAATTATTAGA
AAAGGACATGCTTTTGAAGCTCGAATTTATGCTGAAGATCCTGCTAATAATTTCCTTCCA
GGTGCTGGCCCTTTAAATCATTTAACAACTCCCGAGCCGAGTGATTTTGTTAGAGTTGAA
ACAGGCGTGAGAGAAAATGATGATGTTACAGTTCATTATGATCCAATGATTGCAAAATTA
GTTGTATGGGGTGAAGATAGAAGTTCAGCATTGAATAGTTTGATATCACGATTGAGTGAA
TATCATATAACAGGTCTTGAAACAAATGTTAACTTCCTCATGGATTTAGCTCGTCATGAA
TATTTCCAAAAAGGAGATGTTCATACAGGTTTCATTAATCAACACTTTGATACACTCTTT
CCTCAGAAAGTAATTAAAAATGAAATCTTAGCACAAGCAGCTCTTGGTTTAATTATTAAT
GAAAATAATTCTGCATTAATTAACTCATTAAGAGAAGGAAAATTGAATGATCCGTTTGCA
ATTAATAGTGATTTTAGAATCAATTCAACTCATGTAAGAACTGTGAAGTTTTTTGCTAAT
GAAAAAGAGCAACAAGTGTCAGTTATGCAAATTCAAGACGGTTACAAAGTCAAAGTCAAT
GATGGCGAATGGAAAAATGTTCAAGTTACAAAAGTAAAAGAAGAGGGAAGATTTACATTA
AAAGTCAACATGGAAGGTGTTGTCTACAAATATTCAATTGTAATCACACCAGAGAGTGTC
ACATTATTCAATGAAAGTGGCAAAACTGAGCTACAAATCAAACAACCAAAGTTCTTAGAA
ACAACAAGCGGAAGTGATGGAAGCAAAGCAAGTTTAAGTGCTCCAATGCCTGGAATTATT
GATAAAATTTTCGTCAATGTCGGAGATGAAGTGAAGCCAGGTCAAAGTGTTGCAGTTATT
ATTGCCATGAAGATGGAATATGTTCTTAAAGCAGCTGTAAGTGGCAAAGTCAAATCAATT
GCAGGAAAAATTGGTGACAACATTGGAAAAGGGGTCACAATTGTCGAAATTGAAGCAACA
GAGGAATAA
>g13674.t1 Gene=g13674 Length=702
MLSRAKLFTKLNHHAFMRSFTVKTKPEIKPINKVLIANRGEIAVRVIKTCKKLGIRTVAV
FSDADAKSLHVSMADEAYHIGPALSSKSYLRGDKIIDVAHLTGAQAIHPGYGFLSESVEF
SALCEKTGVIFIGPPESAIRDMGIKSTSKHIMTSAGVPCIMGYHGENQSDDFLVKEAEKI
GYPLMIKAVRGGGGKGMRIANTPEEFLPQLQSARTESEKAFGDSTMLLEKYVRSPRHVEV
QVFADKYGDAVYLWERDCSVQRRHQKIIEEAPAPGISEELRRKLGEAAVRAAKAVNYVGA
GTVEFILDKEDLSFHFMEMNTRLQVEHPITEMITGIDLVDWQIRIASGEPLPLTQEQIIR
KGHAFEARIYAEDPANNFLPGAGPLNHLTTPEPSDFVRVETGVRENDDVTVHYDPMIAKL
VVWGEDRSSALNSLISRLSEYHITGLETNVNFLMDLARHEYFQKGDVHTGFINQHFDTLF
PQKVIKNEILAQAALGLIINENNSALINSLREGKLNDPFAINSDFRINSTHVRTVKFFAN
EKEQQVSVMQIQDGYKVKVNDGEWKNVQVTKVKEEGRFTLKVNMEGVVYKYSIVITPESV
TLFNESGKTELQIKQPKFLETTSGSDGSKASLSAPMPGIIDKIFVNVGDEVKPGQSVAVI
IAMKMEYVLKAAVSGKVKSIAGKIGDNIGKGVTIVEIEATEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13674.t1 | CDD | cd06850 | biotinyl_domain | 632 | 697 | 7.70811E-22 |
| 12 | g13674.t1 | Gene3D | G3DSA:3.30.470.130 | - | 19 | 480 | 3.2E-197 |
| 11 | g13674.t1 | Gene3D | G3DSA:2.40.50.100 | - | 624 | 701 | 1.2E-18 |
| 5 | g13674.t1 | PANTHER | PTHR18866:SF33 | METHYLCROTONOYL-COA CARBOXYLASE SUBUNIT ALPHA, MITOCHONDRIAL-RELATED | 23 | 698 | 2.0E-281 |
| 6 | g13674.t1 | PANTHER | PTHR18866 | CARBOXYLASE:PYRUVATE/ACETYL-COA/PROPIONYL-COA CARBOXYLASE | 23 | 698 | 2.0E-281 |
| 4 | g13674.t1 | Pfam | PF00289 | Biotin carboxylase, N-terminal domain | 31 | 139 | 6.1E-44 |
| 2 | g13674.t1 | Pfam | PF02786 | Carbamoyl-phosphate synthase L chain, ATP binding domain | 145 | 352 | 1.1E-74 |
| 1 | g13674.t1 | Pfam | PF02785 | Biotin carboxylase C-terminal domain | 366 | 473 | 2.6E-34 |
| 3 | g13674.t1 | Pfam | PF00364 | Biotin-requiring enzyme | 632 | 697 | 1.7E-12 |
| 14 | g13674.t1 | ProSitePatterns | PS00867 | Carbamoyl-phosphate synthase subdomain signature 2. | 316 | 323 | - |
| 15 | g13674.t1 | ProSitePatterns | PS00188 | Biotin-requiring enzymes attachment site. | 654 | 671 | - |
| 17 | g13674.t1 | ProSiteProfiles | PS50979 | Biotin carboxylation domain profile. | 30 | 477 | 54.7 |
| 19 | g13674.t1 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 149 | 347 | 51.324 |
| 18 | g13674.t1 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 623 | 698 | 21.254 |
| 16 | g13674.t1 | SMART | SM00878 | Biotin_carb_C_2 | 366 | 473 | 6.8E-49 |
| 7 | g13674.t1 | SUPERFAMILY | SSF52440 | PreATP-grasp domain | 13 | 142 | 6.12E-50 |
| 9 | g13674.t1 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 112 | 378 | 2.86E-67 |
| 8 | g13674.t1 | SUPERFAMILY | SSF51246 | Rudiment single hybrid motif | 361 | 480 | 6.28E-39 |
| 10 | g13674.t1 | SUPERFAMILY | SSF51230 | Single hybrid motif | 625 | 698 | 4.19E-16 |
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:0046872 | metal ion binding | MF |
| GO:0005524 | ATP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K01968 (3-methylcrotonyl-CoA carboxylase alpha 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.
