General information for g13674.t2
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.t2 | TSS | g13674.t2 | 31498318 | 31498318 |
| chr_1 | g13674 | g13674.t2 | isoform | g13674.t2 | 31498550 | 31500776 |
| chr_1 | g13674 | g13674.t2 | exon | g13674.t2.exon1 | 31498550 | 31499073 |
| chr_1 | g13674 | g13674.t2 | cds | g13674.t2.CDS1 | 31498656 | 31499073 |
| chr_1 | g13674 | g13674.t2 | exon | g13674.t2.exon2 | 31499134 | 31500776 |
| chr_1 | g13674 | g13674.t2 | cds | g13674.t2.CDS2 | 31499134 | 31500776 |
| chr_1 | g13674 | g13674.t2 | TTS | g13674.t2 | 31500972 | 31500972 |
Sequences
>g13674.t2 Gene=g13674 Length=2167
ATGTTATCTAGAGCGAAGTAAGTTTTAATTTACTAATCCTTTCATGATAATAAAATTAAA
CTGCGTTTTTTTTAGACTTTTTACAAAATTAAATCATCATGCTTTTATGCGATCATTCAC
AGTAAAAACAAAACCCGAAATAAAACCAATAAATAAAGTTTTAATTGCGAATAGAGGAGA
AATTGCAGTGCGTGTGATTAAAACATGCAAGAAACTTGGTATTCGAACAGTTGCAGTTTT
TTCTGATGCTGATGCAAAATCATTGCATGTGTCTATGGCTGATGAAGCATATCATATTGG
TCCAGCACTTTCATCAAAAAGTTACTTGAGGGGTGATAAAATCATTGATGTTGCACATTT
GACTGGTGCTCAAGCCATTCATCCTGGTTATGGCTTTCTATCAGAAAGTGTAGAATTTTC
AGCATTATGTGAGAAAACAGGTGTAATTTTTATTGGCCCACCTGAGAGTGCGATTAGAGA
TATGGGAATTAAAAGTACATCAAAACATATCATGACATCTGCTGGTGTTCCATGTATAAT
GGGCTATCACGGCGAAAATCAATCAGATGATTTTTTAGTAAAAGAGGCTGAGAAAATTGG
TTATCCTTTAATGATTAAAGCAGTAAGAGGTGGAGGTGGCAAAGGCATGAGAATTGCAAA
CACTCCAGAGGAATTTTTGCCTCAACTTCAAAGTGCTCGAACAGAATCAGAAAAAGCATT
TGGTGATAGCACAATGTTGCTTGAAAAATATGTTCGCAGTCCTCGTCATGTTGAAGTTCA
AGTTTTTGCTGACAAATATGGTGATGCTGTCTATTTATGGGAAAGAGATTGCTCAGTACA
ACGAAGACATCAAAAAATTATTGAAGAAGCTCCTGCACCAGGAATATCAGAAGAATTGAG
AAGAAAATTGGGTGAAGCAGCTGTGAGAGCAGCAAAAGCTGTTAATTATGTTGGCGCAGG
AACAGTTGAATTTATTTTAGATAAAGAAGATTTATCATTCCATTTTATGGAAATGAATAC
AAGATTGCAAGTTGAGCATCCTATTACAGAAATGATTACAGGAATTGATTTAGTTGATTG
GCAAATAAGAATTGCAAGTGGTGAACCATTGCCATTAACTCAAGAACAAATTATTAGAAA
AGGACATGCTTTTGAAGCTCGAATTTATGCTGAAGATCCTGCTAATAATTTCCTTCCAGG
TGCTGGCCCTTTAAATCATTTAACAACTCCCGAGCCGAGTGATTTTGTTAGAGTTGAAAC
AGGCGTGAGAGAAAATGATGATGTTACAGTTCATTATGATCCAATGATTGCAAAATTAGT
TGTATGGGGTGAAGATAGAAGTTCAGCATTGAATAGTTTGATATCACGATTGAGTGAATA
TCATATAACAGGTCTTGAAACAAATGTTAACTTCCTCATGGATTTAGCTCGTCATGAATA
TTTCCAAAAAGGAGATGTTCATACAGGTTTCATTAATCAACACTTTGATACACTCTTTCC
TCAGAAAGTAATTAAAAATGAAATCTTAGCACAAGCAGCTCTTGGTTTAATTATTAATGA
AAATAATTCTGCATTAATTAACTCATTAAGAGAAGGAAAATTGAATGATCCGTTTGCAAT
TAATAGTGATTTTAGAATCAATTCAACTCATGTAAGAACTGTGAAGTTTTTTGCTAATGA
AAAAGAGCAACAAGTGTCAGTTATGCAAATTCAAGACGGTTACAAAGTCAAAGTCAATGA
TGGCGAATGGAAAAATGTTCAAGTTACAAAAGTAAAAGAAGAGGGAAGATTTACATTAAA
AGTCAACATGGAAGGTGTTGTCTACAAATATTCAATTGTAATCACACCAGAGAGTGTCAC
ATTATTCAATGAAAGTGGCAAAACTGAGCTACAAATCAAACAACCAAAGTTCTTAGAAAC
AACAAGCGGAAGTGATGGAAGCAAAGCAAGTTTAAGTGCTCCAATGCCTGGAATTATTGA
TAAAATTTTCGTCAATGTCGGAGATGAAGTGAAGCCAGGTCAAAGTGTTGCAGTTATTAT
TGCCATGAAGATGGAATATGTTCTTAAAGCAGCTGTAAGTGGCAAAGTCAAATCAATTGC
AGGAAAAATTGGTGACAACATTGGAAAAGGGGTCACAATTGTCGAAATTGAAGCAACAGA
GGAATAA
>g13674.t2 Gene=g13674 Length=686
MRSFTVKTKPEIKPINKVLIANRGEIAVRVIKTCKKLGIRTVAVFSDADAKSLHVSMADE
AYHIGPALSSKSYLRGDKIIDVAHLTGAQAIHPGYGFLSESVEFSALCEKTGVIFIGPPE
SAIRDMGIKSTSKHIMTSAGVPCIMGYHGENQSDDFLVKEAEKIGYPLMIKAVRGGGGKG
MRIANTPEEFLPQLQSARTESEKAFGDSTMLLEKYVRSPRHVEVQVFADKYGDAVYLWER
DCSVQRRHQKIIEEAPAPGISEELRRKLGEAAVRAAKAVNYVGAGTVEFILDKEDLSFHF
MEMNTRLQVEHPITEMITGIDLVDWQIRIASGEPLPLTQEQIIRKGHAFEARIYAEDPAN
NFLPGAGPLNHLTTPEPSDFVRVETGVRENDDVTVHYDPMIAKLVVWGEDRSSALNSLIS
RLSEYHITGLETNVNFLMDLARHEYFQKGDVHTGFINQHFDTLFPQKVIKNEILAQAALG
LIINENNSALINSLREGKLNDPFAINSDFRINSTHVRTVKFFANEKEQQVSVMQIQDGYK
VKVNDGEWKNVQVTKVKEEGRFTLKVNMEGVVYKYSIVITPESVTLFNESGKTELQIKQP
KFLETTSGSDGSKASLSAPMPGIIDKIFVNVGDEVKPGQSVAVIIAMKMEYVLKAAVSGK
VKSIAGKIGDNIGKGVTIVEIEATEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g13674.t2 | CDD | cd06850 | biotinyl_domain | 616 | 681 | 1.04819E-21 |
| 12 | g13674.t2 | Gene3D | G3DSA:3.30.470.130 | - | 4 | 464 | 3.2E-197 |
| 11 | g13674.t2 | Gene3D | G3DSA:2.40.50.100 | - | 608 | 685 | 1.2E-18 |
| 5 | g13674.t2 | PANTHER | PTHR18866:SF33 | METHYLCROTONOYL-COA CARBOXYLASE SUBUNIT ALPHA, MITOCHONDRIAL-RELATED | 8 | 682 | 3.3E-281 |
| 6 | g13674.t2 | PANTHER | PTHR18866 | CARBOXYLASE:PYRUVATE/ACETYL-COA/PROPIONYL-COA CARBOXYLASE | 8 | 682 | 3.3E-281 |
| 4 | g13674.t2 | Pfam | PF00289 | Biotin carboxylase, N-terminal domain | 15 | 123 | 5.9E-44 |
| 2 | g13674.t2 | Pfam | PF02786 | Carbamoyl-phosphate synthase L chain, ATP binding domain | 129 | 336 | 1.1E-74 |
| 1 | g13674.t2 | Pfam | PF02785 | Biotin carboxylase C-terminal domain | 350 | 457 | 2.5E-34 |
| 3 | g13674.t2 | Pfam | PF00364 | Biotin-requiring enzyme | 616 | 681 | 1.6E-12 |
| 14 | g13674.t2 | ProSitePatterns | PS00867 | Carbamoyl-phosphate synthase subdomain signature 2. | 300 | 307 | - |
| 15 | g13674.t2 | ProSitePatterns | PS00188 | Biotin-requiring enzymes attachment site. | 638 | 655 | - |
| 17 | g13674.t2 | ProSiteProfiles | PS50979 | Biotin carboxylation domain profile. | 14 | 461 | 54.7 |
| 19 | g13674.t2 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 133 | 331 | 51.324 |
| 18 | g13674.t2 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 607 | 682 | 21.254 |
| 16 | g13674.t2 | SMART | SM00878 | Biotin_carb_C_2 | 350 | 457 | 6.8E-49 |
| 7 | g13674.t2 | SUPERFAMILY | SSF52440 | PreATP-grasp domain | 6 | 126 | 2.09E-49 |
| 9 | g13674.t2 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 96 | 362 | 2.69E-67 |
| 8 | g13674.t2 | SUPERFAMILY | SSF51246 | Rudiment single hybrid motif | 345 | 464 | 6.28E-39 |
| 10 | g13674.t2 | SUPERFAMILY | SSF51230 | Single hybrid motif | 609 | 682 | 4.06E-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.
