General information for g4519.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable citrate synthase 2, 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.t13 | TSS | g4519.t13 | 2974301 | 2974301 |
| chr_2 | g4519 | g4519.t13 | isoform | g4519.t13 | 2975492 | 2976874 |
| chr_2 | g4519 | g4519.t13 | exon | g4519.t13.exon1 | 2975492 | 2975649 |
| chr_2 | g4519 | g4519.t13 | cds | g4519.t13.CDS1 | 2975647 | 2975649 |
| chr_2 | g4519 | g4519.t13 | exon | g4519.t13.exon2 | 2976223 | 2976582 |
| chr_2 | g4519 | g4519.t13 | cds | g4519.t13.CDS2 | 2976223 | 2976582 |
| chr_2 | g4519 | g4519.t13 | exon | g4519.t13.exon3 | 2976650 | 2976874 |
| chr_2 | g4519 | g4519.t13 | cds | g4519.t13.CDS3 | 2976650 | 2976874 |
| chr_2 | g4519 | g4519.t13 | TTS | g4519.t13 | NA | NA |
Sequences
>g4519.t13 Gene=g4519 Length=743
TCTTGCCAGCGATCATAACATGTGTAAGAAACATCTCGGCAGATAGCACCGATTTGAAAG
CAATTTTAGCAGACAAAATTCCAAAGGAACAGGAACGTGTGAAGAACTTCCGCAAAGCTC
ATGGCGCAACAAAAGTTGGCGAAGTTACAATTGATATGATGTATGGTGGCATGCGTGGCA
TTAAAGGTCTTGTCTATGAGACATCTGTCTTGGATCCAGATGAGGGAATTCGTTTCCGTG
GATTATCAATTCCTGAATGCCAGCAAGTTTTGCCAAAAGCTCCAGGCGGTTCTGAGCCAT
TGCCAGAGGGTCTTTTCTGGCTTCTCATTACCGGTGATGTTCCAAATCAACAGCAAGTCA
ATTGGTTGTCACGTGAATGGTCAAATCGTGCTGCACTTCCGGGCCACGTTGTAACAATGC
TCAACAACTTTCCAACAACTCTCCATCCAATGTCACAATTTTCAGCTGCTATCACAGCAT
TGAATCATGACAGCAAATACGCAAAAGCATATTCAGAAGGTGTACACAAAAGCAAATACT
GGGAATATGTCTACGAAGATAGCATGGACTTGATTGCTAAATTGCCAGTTGTAGCTGCAA
CAATTTATCGCAATACTTATCGTGATGGAAAGGGTATTGGAGCAATCGATTCAAAGCTTG
ATTGGTCTGCCAATTTCACTCGTATGCTCGGTTATGATAACGAAGAATTCACCGAATTAA
TGCGTTTATATCTCACCATTCAC
>g4519.t13 Gene=g4519 Length=196
MMYGGMRGIKGLVYETSVLDPDEGIRFRGLSIPECQQVLPKAPGGSEPLPEGLFWLLITG
DVPNQQQVNWLSREWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALNHDSKYAKAYS
EGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDWSANFTRMLGY
DNEEFTELMRLYLTIH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4519.t13 | Gene3D | G3DSA:1.10.580.10 | Citrate Synthase | 1 | 196 | 0e+00 |
| 2 | g4519.t13 | PANTHER | PTHR11739 | CITRATE SYNTHASE | 1 | 196 | 0e+00 |
| 3 | g4519.t13 | PANTHER | PTHR11739:SF29 | CITRATE SYNTHASE | 1 | 196 | 0e+00 |
| 5 | g4519.t13 | PRINTS | PR00143 | Citrate synthase signature | 139 | 152 | 6e-05 |
| 4 | g4519.t13 | PRINTS | PR00143 | Citrate synthase signature | 188 | 196 | 6e-05 |
| 1 | g4519.t13 | Pfam | PF00285 | Citrate synthase, C-terminal domain | 5 | 196 | 0e+00 |
| 6 | g4519.t13 | SUPERFAMILY | SSF48256 | Citrate synthase | 1 | 196 | 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. There were no conditions that were differentially expressed