General information for g4007.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Acyl-CoA synthetase short-chain family member 3, mitochondrial.
Parent gene
- The parent gene g4007 is located on chr_3: 29487106..29493340 (- 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_3 | g4007 | g4007.t1 | isoform | g4007.t1 | 29487106 | 29493340 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon1 | 29487106 | 29487116 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS1 | 29487106 | 29487116 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon2 | 29487185 | 29487405 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS2 | 29487185 | 29487405 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon3 | 29487469 | 29487525 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS3 | 29487469 | 29487525 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon4 | 29487586 | 29487740 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS4 | 29487586 | 29487740 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon5 | 29487801 | 29487814 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS5 | 29487801 | 29487814 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon6 | 29487877 | 29488116 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS6 | 29487877 | 29488116 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon7 | 29488181 | 29488246 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS7 | 29488181 | 29488246 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon8 | 29488318 | 29488756 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS8 | 29488318 | 29488756 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon9 | 29488832 | 29489023 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS9 | 29488832 | 29489023 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon10 | 29489079 | 29489197 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS10 | 29489079 | 29489197 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon11 | 29492718 | 29492862 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS11 | 29492718 | 29492862 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon12 | 29492926 | 29493218 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS12 | 29492926 | 29493218 |
| chr_3 | g4007 | g4007.t1 | exon | g4007.t1.exon13 | 29493274 | 29493340 |
| chr_3 | g4007 | g4007.t1 | cds | g4007.t1.CDS13 | 29493274 | 29493340 |
| chr_3 | g4007 | g4007.t1 | TSS | g4007.t1 | 29493447 | 29493447 |
| chr_3 | g4007 | g4007.t1 | TTS | g4007.t1 | NA | NA |
Sequences
>g4007.t1 Gene=g4007 Length=2019
ATGGCTAAAAGTGTTCAAAAGAAGAATAATGCTACCAATAAAGGAGCAAGTTCGAGACGA
TTTCCAAGTGATCATGATCATCTATACAAAGAAGCATATTTGCGTTCAATAGAAGAACCA
GATAAATTTTGGGATGAAATTGCTTCAACACTTATCTCATGGGATAAAATGTATGATAAA
GTGCTTGATAATAGCAATTCCCCATTTACTAAATGGTTCCTAAATGGACAATTAAATGCA
TGCTTCAATTGTGTGGACAGGCACGTGGCTAACGGCTTAGGAAAAAAGGTTGCATTAATT
CATGACAGTCCTGTAACTAATACAATTCGACGTGTCACTTATGAAGAACTTCTTGATTCA
ATTTCGCGATTAGCAGGCGGATTGAAGAAGCTAGGAGTTGATAAAGGTGATCGAGTAGTC
ATTTATATGCCACTCATCCCTGAAGCAGTGATTAGCATGTTAGCAGTAGTTCGCTTGGGA
GCAATCCATTCAGTAGTTTTTGGAGGTTTTGCATCAAGCGAATTATGTACAAGAATCGAG
CATGCTGAGCCAAAAGTGGTAATTTCAGCCAATTGTGGCGTAGAGCCTAACAAGGTTATT
CCTTATCTCGATATCTTGCATGAGGCAATTGATATGTCTCAATGGAAACCTGATAAATGT
ATCATTTTTCAACGCAAAAATATTTTGGTGTCTGAACTTGACCCTATCATGGATATTTGT
TGGGAAAATACGCTTAGCGAACCAGCTGAGTGTGTTAAAGTTGAAGCAAATGATCCCTTA
TATATTTTATATACATCCGGAACAACTGATAAACCTAAAGGAGTTCAACGTCCAACTGGT
CATATTGTAACACTAATTTATACAATGAATACTATTTACGGTATTCGTCAAAATGATGTT
TGGTGGGCAGCAAGTGATTTAGGTTGGGTTGTTGGACACAGTTACATTGCTTATGGTCCA
CTTCTTTTGGGAGCAACAAGTGTTATGTATGAAGGAAAGCCCGATCGAACACCAGATCCT
GGCCAATATTTTAGAATTATTGAACAGCATCAAGTATCGGCAATCTTTAGTGTTCCAACT
GCTTTTCGTGTCATCAGAAAAGTTGATCCACATGCACGTTATGGTAGCAAATACAGTCTC
AATTCACTACAAAGAATTTTCATTGCTGGCGAACATTGTGATTTAGAGACGAAAAATTGG
ATGGAAAACATTTTCAGAGTGCCTGTTTTAAATCATTGGTGGCAAACTGAAACAGGTTCA
GCAATAACTGCAACTTGTATTGGATTTTCGCAAAATTTGAATGTTCCGAATTTTACTACT
GGATTGCCTTTTGTTGGATATGATGTTAAAGTGATGCAATCTGATGCAAAAGAATTGAAA
GAATTAGGACCTAATCAATTGGGAAGAATTTTATTGAAATTACCATTACCACCTGGCAAC
ATGTCTACGCTTTATAAAAATGATGATCTCTTTGAGAAACTCTACTTTCAACGATTTCCA
GGTTTTTACGATACAATGGATGCAGGCTATAAGGATGAAAGTGGATATGTTTATGTAACA
GCTCGTGACGATGATGTCATAAATGTTGCTGGACATAGGATTTCTACAAGCAGTTTAGAA
GATGCAATATTGAGACATCAAGACGTAGCTGATTGTGCCGTTTTTGGTGTACCTGAGATG
ACAAAGGGTCAAGTGCCACTTTGTCTTTATGTCACTAAAGATGGAGTCAAAAAACCACAA
ACGAAAATCTCTGTTGAAATAATTAAAATTATTAGAGATGTTATTGGACCTATAGCATCT
TTCAAATTAGTTGCTAAAGTTCAAGCGCTTCCACGAACAAGAAGTGGTAAAACGATGAGA
AAAGCATTAGCTGATTTTGCTCGCAACAAGACAGTAAATTTACCAGCAACCATCGAAGAT
CCAACGGTTTTCATTGATATTCGTAGAGCATTGAATGAATTGGGCTATGCTAATTCTGCA
CCATCACCACTCGTTGGTTACAAAAAACGGTCAATTTAA
>g4007.t1 Gene=g4007 Length=672
MAKSVQKKNNATNKGASSRRFPSDHDHLYKEAYLRSIEEPDKFWDEIASTLISWDKMYDK
VLDNSNSPFTKWFLNGQLNACFNCVDRHVANGLGKKVALIHDSPVTNTIRRVTYEELLDS
ISRLAGGLKKLGVDKGDRVVIYMPLIPEAVISMLAVVRLGAIHSVVFGGFASSELCTRIE
HAEPKVVISANCGVEPNKVIPYLDILHEAIDMSQWKPDKCIIFQRKNILVSELDPIMDIC
WENTLSEPAECVKVEANDPLYILYTSGTTDKPKGVQRPTGHIVTLIYTMNTIYGIRQNDV
WWAASDLGWVVGHSYIAYGPLLLGATSVMYEGKPDRTPDPGQYFRIIEQHQVSAIFSVPT
AFRVIRKVDPHARYGSKYSLNSLQRIFIAGEHCDLETKNWMENIFRVPVLNHWWQTETGS
AITATCIGFSQNLNVPNFTTGLPFVGYDVKVMQSDAKELKELGPNQLGRILLKLPLPPGN
MSTLYKNDDLFEKLYFQRFPGFYDTMDAGYKDESGYVYVTARDDDVINVAGHRISTSSLE
DAILRHQDVADCAVFGVPEMTKGQVPLCLYVTKDGVKKPQTKISVEIIKIIRDVIGPIAS
FKLVAKVQALPRTRSGKTMRKALADFARNKTVNLPATIEDPTVFIDIRRALNELGYANSA
PSPLVGYKKRSI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4007.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 55 | 522 | 2.4E-88 |
| 11 | g4007.t1 | Gene3D | G3DSA:3.30.300.30 | - | 525 | 654 | 2.3E-20 |
| 8 | g4007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 9 | g4007.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 4 | g4007.t1 | PANTHER | PTHR43347 | ACYL-COA SYNTHETASE | 26 | 655 | 1.1E-269 |
| 5 | g4007.t1 | PANTHER | PTHR43347:SF3 | ACYL-COA SYNTHETASE SHORT-CHAIN FAMILY MEMBER 3, MITOCHONDRIAL | 26 | 655 | 1.1E-269 |
| 2 | g4007.t1 | Pfam | PF16177 | Acetyl-coenzyme A synthetase N-terminus | 29 | 84 | 1.8E-21 |
| 3 | g4007.t1 | Pfam | PF00501 | AMP-binding enzyme | 89 | 529 | 3.8E-78 |
| 1 | g4007.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 539 | 617 | 1.7E-17 |
| 7 | g4007.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 28 | 630 | 1.05E-138 |
| 6 | g4007.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 161 | - |
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 K01908 (propionyl-CoA synthetase)
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.
