General information for g4300.t2
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.t2 | TSS | g4300.t2 | 1087998 | 1087998 |
| chr_2 | g4300 | g4300.t2 | isoform | g4300.t2 | 1088100 | 1090433 |
| chr_2 | g4300 | g4300.t2 | exon | g4300.t2.exon1 | 1088100 | 1088551 |
| chr_2 | g4300 | g4300.t2 | cds | g4300.t2.CDS1 | 1088536 | 1088551 |
| chr_2 | g4300 | g4300.t2 | exon | g4300.t2.exon2 | 1088616 | 1090433 |
| chr_2 | g4300 | g4300.t2 | cds | g4300.t2.CDS2 | 1088616 | 1090108 |
| chr_2 | g4300 | g4300.t2 | TTS | g4300.t2 | 1090427 | 1090427 |
Sequences
>g4300.t2 Gene=g4300 Length=2270
ATGATTCGGATTCAGCAAAGAAATTTGATTAAATTTTTTTCAAACAGCAGAACACTTTCG
TCATCCAATTTAAATCCAAATTTCGATTCTTCAAATTCATCTTCTCAAGAGTCAAAAGTA
CAGCAGCTTATTAATGCAGATTTGAAATGTAATAATCCAGTGCCAGTATTTAAGCGAGCC
CTTTTAAACAGCCAAAAAACTGCAATCAAAGACATTAATGGCGAAAAAACATATTTAGAA
CTGATTTCGGGGTCATTTAAATTGTCAAAACAAATCTCGGATGTATGCGGTAAGTCGTTT
GTTGATTAACATACATTCGTTCTGCTAAAAATAATTATTTTTCTACCTTCTTTTCACAGC
TAAAGAATCACTTGCTAAAGTAGCATTTCTCTGTAATAATGACATATCTTATATACTTTC
GCAATGGGCTACTTGGATGTCTGGTCAAATCGCCATTCCACTTAGTACAGCTCATCCCGT
TGAACTTTTAGAATTTTACATTCAAGATTCAGAGACCAATCTCATTATAACTACACCACA
ATATGAAGAAAAATTAAAACCATTGGCAGATAAATTGAAAAAACCACTTCATGTAATTGA
TCAGGCAGCTTTAATTGATGCTGAATCTACAAATCTTGATGAGGAATCGCTTCTATGTAA
TTTACCAAAAGGATCCTTTTATAAAAAATCTCCAGCTTTATTCTTATACACGAGTGGTAC
AACTTCAAAGCCTAAAGGTGTTCAAATGACATATTCAAACCTTGAAGCACAAGTTTCTAG
TTTACAACATGCGTGGAATATTCAGTCAACGGATACTATTCTTCATGCTTTACCACTGCA
TCATACACATGGTATAATTAATGCACTGTTGCTTCCTTTGAGTGCTGGTGGAAAAGTTAT
CATGTTACCGAAATTCGAATCAGATAATGTGTGGTCACATCTTTTAAACATCAATATGCC
GCAAAAAGATCGTGTGACAGTTTTCATGGGAATTCCAACTATATTTAATTATCTTATTCA
AGAATATGATAAGCTCTTTAGCAAATCCTCACAAATGACGGAATATATCAAGACACATTG
TCAAAACAAAATTCGTTTAATGATTTGCGGCAGTGCACCTCTTCCTAATACAGTTTTTCA
ACGATGGAAAGATATTACAGGTCATAAGTTATTAGAACGTTATGGAATGACAGAGATTGG
TATGTGTTTAAGCAATCCTTTAACAGAAAACAAAGTGAGACAGCGATTGCCAGGTTTCGT
TGGTCAACCATTACCAGGAGTCAAAGTACGCGTAGCAAATGCAGAAAATCCTAAAGACAT
TCTTCTTGAGGCAAGCGGTGAATATAACAAGGGAATTTGGTCACAAGAGCAAGAAGATAA
GGCTGTTGTAAAAATTAAACAAGGATTGGCAAGTGATGCAGAAATTATTGGCAGTCTTCA
AGTGCAAGGACCTAGTGTATTTAAAGAATACTGGAATCGTGAATCGGTAACTAAAGAAGC
TTTCACAGAAGATGGTTTTTTTATAACTGGTGATACAGCTTGTTATGATCCAACAGTAAA
CAGCTTTAAAATAATGGGCAGAAATTCTGTTGATATTCTTAAATCTAAAGGATATAAGAT
ATCAGCGTTAGAAATTGAAACAAAGTTATTAGAGAATCCCTTAATTGAAGATTGTGCAGT
TATTGGTGTGCCAGATGAAGTTCTTGGTCAGAAAATTATTGCATTAATAGTAAAACGCGT
GAATAAAACGGCAGACGAAAGTACAGTGAATGAAACAGATAACTTGCTAACGTTAAAAAA
ATGGTGTGAGAGTAAATTTGCTTCCTACAGTATGCCAACACTAACATTTGTCAGTAGAAT
ACCAAGAAATCAATTAGGAAAAGTAAACAAGGCCGAGTTAGTGAAGGATTTTGTAAAGAA
GGCCAACGAGGTACCTGCAAAGTGAATTGAACACTCTAAAACTAGTTTTACTAAATTCAT
GTGTTCCTTTTTGATTCGGAGTTCTTTTTCATTGCAAAATTACTTCTTTTGGCATAAAAT
TAAATGTATTGGAATAAAAAGTTATTTTGCTGCGAACTAGTCAAAGCAAGAAAAGATCAA
TTTCATGAATTCATCTCACAGGTCATACTCTAATTAGAAGCATTTTATTACTTTCATTAT
CGCGTTTAAATTATTATTTACGAAAAAATTTATTTTGCTTATTCTATCTTATTAAAATTG
ATTGTTGATAATACGACTTGATAAATAAATTCACATGTGAATCAAAATAA
>g4300.t2 Gene=g4300 Length=502
MSGQIAIPLSTAHPVELLEFYIQDSETNLIITTPQYEEKLKPLADKLKKPLHVIDQAALI
DAESTNLDEESLLCNLPKGSFYKKSPALFLYTSGTTSKPKGVQMTYSNLEAQVSSLQHAW
NIQSTDTILHALPLHHTHGIINALLLPLSAGGKVIMLPKFESDNVWSHLLNINMPQKDRV
TVFMGIPTIFNYLIQEYDKLFSKSSQMTEYIKTHCQNKIRLMICGSAPLPNTVFQRWKDI
TGHKLLERYGMTEIGMCLSNPLTENKVRQRLPGFVGQPLPGVKVRVANAENPKDILLEAS
GEYNKGIWSQEQEDKAVVKIKQGLASDAEIIGSLQVQGPSVFKEYWNRESVTKEAFTEDG
FFITGDTACYDPTVNSFKIMGRNSVDILKSKGYKISALEIETKLLENPLIEDCAVIGVPD
EVLGQKIIALIVKRVNKTADESTVNETDNLLTLKKWCESKFASYSMPTLTFVSRIPRNQL
GKVNKAELVKDFVKKANEVPAK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4300.t2 | Gene3D | G3DSA:3.40.50.12780 | - | 1 | 382 | 2.6E-79 |
| 8 | g4300.t2 | Gene3D | G3DSA:3.30.300.310 | - | 386 | 498 | 3.7E-22 |
| 3 | g4300.t2 | PANTHER | PTHR24096:SF267 | ACYL-COA SYNTHETASE FAMILY MEMBER 3, MITOCHONDRIAL | 1 | 490 | 5.9E-140 |
| 4 | g4300.t2 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 1 | 490 | 5.9E-140 |
| 2 | g4300.t2 | Pfam | PF00501 | AMP-binding enzyme | 3 | 383 | 4.7E-61 |
| 1 | g4300.t2 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 399 | 482 | 1.4E-10 |
| 6 | g4300.t2 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 89 | 100 | - |
| 5 | g4300.t2 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 2 | 494 | 1.7E-91 |
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.
