General information for g5254.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Fatty acid synthase.
Parent gene
- The parent gene g5254 is located on chr_2: 8162571..8163710 (- 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 | g5254 | g5254.t2 | TTS | g5254.t2 | 8161922 | 8161922 |
| chr_2 | g5254 | g5254.t2 | isoform | g5254.t2 | 8162571 | 8163710 |
| chr_2 | g5254 | g5254.t2 | exon | g5254.t2.exon1 | 8162571 | 8162909 |
| chr_2 | g5254 | g5254.t2 | cds | g5254.t2.CDS1 | 8162573 | 8162909 |
| chr_2 | g5254 | g5254.t2 | exon | g5254.t2.exon2 | 8162965 | 8163037 |
| chr_2 | g5254 | g5254.t2 | cds | g5254.t2.CDS2 | 8162965 | 8163037 |
| chr_2 | g5254 | g5254.t2 | exon | g5254.t2.exon3 | 8163109 | 8163239 |
| chr_2 | g5254 | g5254.t2 | cds | g5254.t2.CDS3 | 8163109 | 8163239 |
| chr_2 | g5254 | g5254.t2 | exon | g5254.t2.exon4 | 8163295 | 8163710 |
| chr_2 | g5254 | g5254.t2 | cds | g5254.t2.CDS4 | 8163295 | 8163710 |
| chr_2 | g5254 | g5254.t2 | TSS | g5254.t2 | 8163814 | 8163814 |
Sequences
>g5254.t2 Gene=g5254 Length=959
ATGTGTGAAAGTGAAGATGATATTGTCATTAGTGGAATTTCTGGGCGATTTCCAAAGTCA
AGAAATGTGCAAGAATTTTGTAAAAATCTTTATGGGAAAGTTGATATGACTTGTGATAAA
GAAGATCGTTGGAAGCATGTTTTTCCTAATGTTCCACCAAGGTTTGGAAAAATTACAGAT
ATTGAGAAGTTTGATGCACCATTTTTTTCAATGCTTAAAAAACATGCTGAATGGACTGAT
CCACAAATGAGAATGCTGCTTGAACACTCGTATGAAGCAATTTTAGATGCTGGAATTAGT
CCACAGTCATTAATGGGTAGTAAAACTGCAGTGCTTGTCGGTGTTGTGAGTTCTGATTCA
AAAGATTATTTTTCTAAAAATATACTGCCGACTTATCATGGTTATCGTGTTGTTGGTCAT
GCACTCTGTTATCTCGCAAATCGAGTTTCTTATTTATTTGGATTGACCGGACCTTCAATG
GTTATCGACACAGCTTGTTCTAGTTCTGCATGTGCTTTAGATATGGCATATTATTATTTA
AAATCAGGAGTTTGTGATGCAGCAATTGTTGGTGGACTTCAATTAAATTTAAATACAACA
ACTTTCACTGAATATACAGGCTTAGGAATTCTTTCACCTGATGGCATCCCTAGACCTTAC
GATGAAGATGCTACAGGATTTACTCGTGCTGAATCAATTTGTTCAGTATTTCTTCAAAAA
AGAAAAGATTCAAAAAGAATTTATGCTCAACTTGTGCATTCTTTATCAAATAATGATGGT
TTTAAAATTGAAGGTCAATCATTGCCATCGAGAGAAATGCAAGTCAAATTAATGGATGAT
TTTTATCAAAAAGTCAATGTTGATATTCGTGATGTGAAATTTATTGAAGCTCATGCAACT
GGCACTAAAAAAGGTGATCCTTTAGAAGTTTCAGCAATTGATGAAGTTTTATGCAAAAA
>g5254.t2 Gene=g5254 Length=319
MCESEDDIVISGISGRFPKSRNVQEFCKNLYGKVDMTCDKEDRWKHVFPNVPPRFGKITD
IEKFDAPFFSMLKKHAEWTDPQMRMLLEHSYEAILDAGISPQSLMGSKTAVLVGVVSSDS
KDYFSKNILPTYHGYRVVGHALCYLANRVSYLFGLTGPSMVIDTACSSSACALDMAYYYL
KSGVCDAAIVGGLQLNLNTTTFTEYTGLGILSPDGIPRPYDEDATGFTRAESICSVFLQK
RKDSKRIYAQLVHSLSNNDGFKIEGQSLPSREMQVKLMDDFYQKVNVDIRDVKFIEAHAT
GTKKGDPLEVSAIDEVLCK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5254.t2 | CDD | cd00833 | PKS | 6 | 319 | 7.94628E-107 |
| 9 | g5254.t2 | Gene3D | G3DSA:3.40.47.10 | - | 4 | 319 | 2.7E-97 |
| 3 | g5254.t2 | PANTHER | PTHR43775 | FATTY ACID SYNTHASE | 5 | 319 | 5.5E-121 |
| 4 | g5254.t2 | PANTHER | PTHR43775:SF23 | FATTY ACID SYNTHASE 3 | 5 | 319 | 5.5E-121 |
| 2 | g5254.t2 | Pfam | PF00109 | Beta-ketoacyl synthase, N-terminal domain | 6 | 243 | 2.1E-55 |
| 1 | g5254.t2 | Pfam | PF02801 | Beta-ketoacyl synthase, C-terminal domain | 248 | 318 | 1.8E-13 |
| 8 | g5254.t2 | ProSitePatterns | PS00606 | Beta-ketoacyl synthases active site. | 157 | 173 | - |
| 7 | g5254.t2 | SMART | SM00825 | Beta-ketoacyl synthase | 8 | 319 | 3.2E-38 |
| 6 | g5254.t2 | SUPERFAMILY | SSF53901 | Thiolase-like | 6 | 246 | 1.0E-53 |
| 5 | g5254.t2 | SUPERFAMILY | SSF53901 | Thiolase-like | 212 | 318 | 2.06E-21 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5254/g5254.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5254.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016746 | acyltransferase activity | MF |
| GO:0004315 | 3-oxoacyl-[acyl-carrier-protein] synthase activity | MF |
| GO:0006633 | fatty acid biosynthetic process | BP |
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. There were no conditions that were differentially expressed