General information for g4519.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable citrate synthase 1, mitochondrial.
Parent gene
- The parent gene g4519 is located on chr_2: 2976951..2978271 (+ 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 | g4519 | g4519.t3 | TSS | g4519.t3 | 2974301 | 2974301 |
| chr_2 | g4519 | g4519.t3 | isoform | g4519.t3 | 2974357 | 2976876 |
| chr_2 | g4519 | g4519.t3 | exon | g4519.t3.exon1 | 2974357 | 2974407 |
| chr_2 | g4519 | g4519.t3 | cds | g4519.t3.CDS1 | 2974357 | 2974407 |
| chr_2 | g4519 | g4519.t3 | exon | g4519.t3.exon2 | 2975488 | 2975649 |
| chr_2 | g4519 | g4519.t3 | cds | g4519.t3.CDS2 | 2975488 | 2975649 |
| chr_2 | g4519 | g4519.t3 | exon | g4519.t3.exon3 | 2976223 | 2976582 |
| chr_2 | g4519 | g4519.t3 | cds | g4519.t3.CDS3 | 2976223 | 2976582 |
| chr_2 | g4519 | g4519.t3 | exon | g4519.t3.exon4 | 2976650 | 2976876 |
| chr_2 | g4519 | g4519.t3 | cds | g4519.t3.CDS4 | 2976650 | 2976874 |
| chr_2 | g4519 | g4519.t3 | TTS | g4519.t3 | NA | NA |
Sequences
>g4519.t3 Gene=g4519 Length=800
ATGGCTTTATTCAGAATTTCATCTACTAAATGCCTAACTGAGGTTCATCAGAGATTCTTG
CCAGCGATCATAACATGTGTAAGAAACATCTCGGCAGATAGCACCGATTTGAAAGCAATT
TTAGCAGACAAAATTCCAAAGGAACAGGAACGTGTGAAGAACTTCCGCAAAGCTCATGGC
GCAACAAAAGTTGGCGAAGTTACAATTGATATGATGTATGGTGGCATGCGTGGCATTAAA
GGTCTTGTCTATGAGACATCTGTCTTGGATCCAGATGAGGGAATTCGTTTCCGTGGATTA
TCAATTCCTGAATGCCAGCAAGTTTTGCCAAAAGCTCCAGGCGGTTCTGAGCCATTGCCA
GAGGGTCTTTTCTGGCTTCTCATTACCGGTGATGTTCCAAATCAACAGCAAGTCAATTGG
TTGTCACGTGAATGGTCAAATCGTGCTGCACTTCCGGGCCACGTTGTAACAATGCTCAAC
AACTTTCCAACAACTCTCCATCCAATGTCACAATTTTCAGCTGCTATCACAGCATTGAAT
CATGACAGCAAATACGCAAAAGCATATTCAGAAGGTGTACACAAAAGCAAATACTGGGAA
TATGTCTACGAAGATAGCATGGACTTGATTGCTAAATTGCCAGTTGTAGCTGCAACAATT
TATCGCAATACTTATCGTGATGGAAAGGGTATTGGAGCAATCGATTCAAAGCTTGATTGG
TCTGCCAATTTCACTCGTATGCTCGGTTATGATAACGAAGAATTCACCGAATTAATGCGT
TTATATCTCACCATTCACAG
>g4519.t3 Gene=g4519 Length=266
MALFRISSTKCLTEVHQRFLPAIITCVRNISADSTDLKAILADKIPKEQERVKNFRKAHG
ATKVGEVTIDMMYGGMRGIKGLVYETSVLDPDEGIRFRGLSIPECQQVLPKAPGGSEPLP
EGLFWLLITGDVPNQQQVNWLSREWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALN
HDSKYAKAYSEGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDW
SANFTRMLGYDNEEFTELMRLYLTIH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4519.t3 | Gene3D | G3DSA:1.10.580.10 | Citrate Synthase | 34 | 266 | 0.0e+00 |
| 2 | g4519.t3 | PANTHER | PTHR11739 | CITRATE SYNTHASE | 45 | 266 | 0.0e+00 |
| 3 | g4519.t3 | PANTHER | PTHR11739:SF29 | CITRATE SYNTHASE | 45 | 266 | 0.0e+00 |
| 4 | g4519.t3 | PRINTS | PR00143 | Citrate synthase signature | 209 | 222 | 9.6e-05 |
| 5 | g4519.t3 | PRINTS | PR00143 | Citrate synthase signature | 258 | 266 | 9.6e-05 |
| 1 | g4519.t3 | Pfam | PF00285 | Citrate synthase, C-terminal domain | 75 | 266 | 0.0e+00 |
| 6 | g4519.t3 | SUPERFAMILY | SSF48256 | Citrate synthase | 34 | 266 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046912 | acyltransferase, acyl groups converted into alkyl on transfer | MF |
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.
