General information for g4300.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Malonate–CoA ligase ACSF3, mitochondrial.
Parent gene
- The parent gene g4300 is located on chr_2: 1088700..1090437 (+ 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_2 | g4300 | g4300.t1 | TSS | g4300.t1 | 1087998 | 1087998 |
| chr_2 | g4300 | g4300.t1 | isoform | g4300.t1 | 1088100 | 1090108 |
| chr_2 | g4300 | g4300.t1 | exon | g4300.t1.exon1 | 1088100 | 1088388 |
| chr_2 | g4300 | g4300.t1 | cds | g4300.t1.CDS1 | 1088100 | 1088388 |
| chr_2 | g4300 | g4300.t1 | exon | g4300.t1.exon2 | 1088459 | 1088551 |
| chr_2 | g4300 | g4300.t1 | cds | g4300.t1.CDS2 | 1088459 | 1088551 |
| chr_2 | g4300 | g4300.t1 | exon | g4300.t1.exon3 | 1088616 | 1090108 |
| chr_2 | g4300 | g4300.t1 | cds | g4300.t1.CDS3 | 1088616 | 1090108 |
| chr_2 | g4300 | g4300.t1 | TTS | g4300.t1 | 1090427 | 1090427 |
Sequences
>g4300.t1 Gene=g4300 Length=1875
ATGATTCGGATTCAGCAAAGAAATTTGATTAAATTTTTTTCAAACAGCAGAACACTTTCG
TCATCCAATTTAAATCCAAATTTCGATTCTTCAAATTCATCTTCTCAAGAGTCAAAAGTA
CAGCAGCTTATTAATGCAGATTTGAAATGTAATAATCCAGTGCCAGTATTTAAGCGAGCC
CTTTTAAACAGCCAAAAAACTGCAATCAAAGACATTAATGGCGAAAAAACATATTTAGAA
CTGATTTCGGGGTCATTTAAATTGTCAAAACAAATCTCGGATGTATGCGCTAAAGAATCA
CTTGCTAAAGTAGCATTTCTCTGTAATAATGACATATCTTATATACTTTCGCAATGGGCT
ACTTGGATGTCTGGTCAAATCGCCATTCCACTTAGTACAGCTCATCCCGTTGAACTTTTA
GAATTTTACATTCAAGATTCAGAGACCAATCTCATTATAACTACACCACAATATGAAGAA
AAATTAAAACCATTGGCAGATAAATTGAAAAAACCACTTCATGTAATTGATCAGGCAGCT
TTAATTGATGCTGAATCTACAAATCTTGATGAGGAATCGCTTCTATGTAATTTACCAAAA
GGATCCTTTTATAAAAAATCTCCAGCTTTATTCTTATACACGAGTGGTACAACTTCAAAG
CCTAAAGGTGTTCAAATGACATATTCAAACCTTGAAGCACAAGTTTCTAGTTTACAACAT
GCGTGGAATATTCAGTCAACGGATACTATTCTTCATGCTTTACCACTGCATCATACACAT
GGTATAATTAATGCACTGTTGCTTCCTTTGAGTGCTGGTGGAAAAGTTATCATGTTACCG
AAATTCGAATCAGATAATGTGTGGTCACATCTTTTAAACATCAATATGCCGCAAAAAGAT
CGTGTGACAGTTTTCATGGGAATTCCAACTATATTTAATTATCTTATTCAAGAATATGAT
AAGCTCTTTAGCAAATCCTCACAAATGACGGAATATATCAAGACACATTGTCAAAACAAA
ATTCGTTTAATGATTTGCGGCAGTGCACCTCTTCCTAATACAGTTTTTCAACGATGGAAA
GATATTACAGGTCATAAGTTATTAGAACGTTATGGAATGACAGAGATTGGTATGTGTTTA
AGCAATCCTTTAACAGAAAACAAAGTGAGACAGCGATTGCCAGGTTTCGTTGGTCAACCA
TTACCAGGAGTCAAAGTACGCGTAGCAAATGCAGAAAATCCTAAAGACATTCTTCTTGAG
GCAAGCGGTGAATATAACAAGGGAATTTGGTCACAAGAGCAAGAAGATAAGGCTGTTGTA
AAAATTAAACAAGGATTGGCAAGTGATGCAGAAATTATTGGCAGTCTTCAAGTGCAAGGA
CCTAGTGTATTTAAAGAATACTGGAATCGTGAATCGGTAACTAAAGAAGCTTTCACAGAA
GATGGTTTTTTTATAACTGGTGATACAGCTTGTTATGATCCAACAGTAAACAGCTTTAAA
ATAATGGGCAGAAATTCTGTTGATATTCTTAAATCTAAAGGATATAAGATATCAGCGTTA
GAAATTGAAACAAAGTTATTAGAGAATCCCTTAATTGAAGATTGTGCAGTTATTGGTGTG
CCAGATGAAGTTCTTGGTCAGAAAATTATTGCATTAATAGTAAAACGCGTGAATAAAACG
GCAGACGAAAGTACAGTGAATGAAACAGATAACTTGCTAACGTTAAAAAAATGGTGTGAG
AGTAAATTTGCTTCCTACAGTATGCCAACACTAACATTTGTCAGTAGAATACCAAGAAAT
CAATTAGGAAAAGTAAACAAGGCCGAGTTAGTGAAGGATTTTGTAAAGAAGGCCAACGAG
GTACCTGCAAAGTGA
>g4300.t1 Gene=g4300 Length=624
MIRIQQRNLIKFFSNSRTLSSSNLNPNFDSSNSSSQESKVQQLINADLKCNNPVPVFKRA
LLNSQKTAIKDINGEKTYLELISGSFKLSKQISDVCAKESLAKVAFLCNNDISYILSQWA
TWMSGQIAIPLSTAHPVELLEFYIQDSETNLIITTPQYEEKLKPLADKLKKPLHVIDQAA
LIDAESTNLDEESLLCNLPKGSFYKKSPALFLYTSGTTSKPKGVQMTYSNLEAQVSSLQH
AWNIQSTDTILHALPLHHTHGIINALLLPLSAGGKVIMLPKFESDNVWSHLLNINMPQKD
RVTVFMGIPTIFNYLIQEYDKLFSKSSQMTEYIKTHCQNKIRLMICGSAPLPNTVFQRWK
DITGHKLLERYGMTEIGMCLSNPLTENKVRQRLPGFVGQPLPGVKVRVANAENPKDILLE
ASGEYNKGIWSQEQEDKAVVKIKQGLASDAEIIGSLQVQGPSVFKEYWNRESVTKEAFTE
DGFFITGDTACYDPTVNSFKIMGRNSVDILKSKGYKISALEIETKLLENPLIEDCAVIGV
PDEVLGQKIIALIVKRVNKTADESTVNETDNLLTLKKWCESKFASYSMPTLTFVSRIPRN
QLGKVNKAELVKDFVKKANEVPAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4300.t1 | CDD | cd05941 | MCS | 65 | 612 | 4.34809E-170 |
| 7 | g4300.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 58 | 504 | 3.9E-86 |
| 8 | g4300.t1 | Gene3D | G3DSA:3.30.300.310 | - | 508 | 620 | 5.3E-22 |
| 3 | g4300.t1 | PANTHER | PTHR24096:SF267 | ACYL-COA SYNTHETASE FAMILY MEMBER 3, MITOCHONDRIAL | 57 | 612 | 4.7E-156 |
| 4 | g4300.t1 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 57 | 612 | 4.7E-156 |
| 2 | g4300.t1 | Pfam | PF00501 | AMP-binding enzyme | 63 | 505 | 1.5E-66 |
| 1 | g4300.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 521 | 604 | 1.9E-10 |
| 6 | g4300.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 211 | 222 | - |
| 5 | g4300.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 57 | 616 | 1.23E-99 |
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 transcript has been annotated with K18660 (malonyl-CoA/methylmalonyl-CoA synthetase [EC:6.2.1.-])
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.
