General information for g4300.t3
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.t3 | TSS | g4300.t3 | 1087942 | 1087942 |
| chr_2 | g4300 | g4300.t3 | isoform | g4300.t3 | 1088100 | 1090437 |
| chr_2 | g4300 | g4300.t3 | exon | g4300.t3.exon1 | 1088100 | 1088388 |
| chr_2 | g4300 | g4300.t3 | cds | g4300.t3.CDS1 | 1088100 | 1088388 |
| chr_2 | g4300 | g4300.t3 | TTS | g4300.t3 | 1088292 | 1088292 |
| chr_2 | g4300 | g4300.t3 | exon | g4300.t3.exon2 | 1088459 | 1088551 |
| chr_2 | g4300 | g4300.t3 | cds | g4300.t3.CDS2 | 1088459 | 1088551 |
| chr_2 | g4300 | g4300.t3 | exon | g4300.t3.exon3 | 1088616 | 1089761 |
| chr_2 | g4300 | g4300.t3 | cds | g4300.t3.CDS3 | 1088616 | 1089761 |
| chr_2 | g4300 | g4300.t3 | exon | g4300.t3.exon4 | 1090018 | 1090437 |
| chr_2 | g4300 | g4300.t3 | cds | g4300.t3.CDS4 | 1090018 | 1090040 |
Sequences
>g4300.t3 Gene=g4300 Length=1948
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
ATAATGGGCAGAAATTCTGTTGATATTCTAGAATACCAAGAAATCAATTAGGAAAAGTAA
ACAAGGCCGAGTTAGTGAAGGATTTTGTAAAGAAGGCCAACGAGGTACCTGCAAAGTGAA
TTGAACACTCTAAAACTAGTTTTACTAAATTCATGTGTTCCTTTTTGATTCGGAGTTCTT
TTTCATTGCAAAATTACTTCTTTTGGCATAAAATTAAATGTATTGGAATAAAAAGTTATT
TTGCTGCGAACTAGTCAAAGCAAGAAAAGATCAATTTCATGAATTCATCTCACAGGTCAT
ACTCTAATTAGAAGCATTTTATTACTTTCATTATCGCGTTTAAATTATTATTTACGAAAA
AATTTATTTTGCTTATTCTATCTTATTAAAATTGATTGTTGATAATACGACTTGATAAAT
AAATTCACATGTGAATCAAAATAATAAA
>g4300.t3 Gene=g4300 Length=516
MIRIQQRNLIKFFSNSRTLSSSNLNPNFDSSNSSSQESKVQQLINADLKCNNPVPVFKRA
LLNSQKTAIKDINGEKTYLELISGSFKLSKQISDVCAKESLAKVAFLCNNDISYILSQWA
TWMSGQIAIPLSTAHPVELLEFYIQDSETNLIITTPQYEEKLKPLADKLKKPLHVIDQAA
LIDAESTNLDEESLLCNLPKGSFYKKSPALFLYTSGTTSKPKGVQMTYSNLEAQVSSLQH
AWNIQSTDTILHALPLHHTHGIINALLLPLSAGGKVIMLPKFESDNVWSHLLNINMPQKD
RVTVFMGIPTIFNYLIQEYDKLFSKSSQMTEYIKTHCQNKIRLMICGSAPLPNTVFQRWK
DITGHKLLERYGMTEIGMCLSNPLTENKVRQRLPGFVGQPLPGVKVRVANAENPKDILLE
ASGEYNKGIWSQEQEDKAVVKIKQGLASDAEIIGSLQVQGPSVFKEYWNRESVTKEAFTE
DGFFITGDTACYDPTVNSFKIMGRNSVDILEYQEIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4300.t3 | Gene3D | G3DSA:3.40.50.12780 | - | 58 | 504 | 2.1E-86 |
| 2 | g4300.t3 | PANTHER | PTHR24096:SF267 | ACYL-COA SYNTHETASE FAMILY MEMBER 3, MITOCHONDRIAL | 57 | 510 | 1.5E-126 |
| 3 | g4300.t3 | PANTHER | PTHR24096 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 57 | 510 | 1.5E-126 |
| 1 | g4300.t3 | Pfam | PF00501 | AMP-binding enzyme | 63 | 504 | 9.3E-67 |
| 5 | g4300.t3 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 211 | 222 | - |
| 4 | g4300.t3 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 57 | 505 | 5.49E-76 |
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 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.
