General information for g4519.t17
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.t17 | isoform | g4519.t17 | 2976650 | 2978271 |
| chr_2 | g4519 | g4519.t17 | exon | g4519.t17.exon1 | 2976650 | 2976876 |
| chr_2 | g4519 | g4519.t17 | cds | g4519.t17.CDS1 | 2976695 | 2976876 |
| chr_2 | g4519 | g4519.t17 | exon | g4519.t17.exon2 | 2976941 | 2978271 |
| chr_2 | g4519 | g4519.t17 | cds | g4519.t17.CDS2 | 2976941 | 2977550 |
| chr_2 | g4519 | g4519.t17 | TTS | g4519.t17 | 2978267 | 2978267 |
| chr_2 | g4519 | g4519.t17 | TSS | g4519.t17 | NA | NA |
Sequences
>g4519.t17 Gene=g4519 Length=1558
GGTGTACACAAAAGCAAATACTGGGAATATGTCTACGAAGATAGCATGGACTTGATTGCT
AAATTGCCAGTTGTAGCTGCAACAATTTATCGCAATACTTATCGTGATGGAAAGGGTATT
GGAGCAATCGATTCAAAGCTTGATTGGTCTGCCAATTTCACTCGTATGCTCGGTTATGAT
AACGAAGAATTCACCGAATTAATGCGTTTATATCTCACCATTCACAGTGATCATGAGGGT
GGCAATGTTAGCGCACACACAGTTCATCTTGTTGGATCAGCACTTAGTGATCCATATCTC
TCATTCGCTGCCGGCATGAATGGTTTGGCTGGTCCACTTCACGGTTTAGCTAATCAAGAA
GTATTGGTTTGGATTCAAAAATTACGTAGTGAACTCGGTGATAATGCATCAGAAGATAAA
GTTAAGGACTTTATCTGGAAGACACTTAAATCAGGTCAAGTTGTTCCAGGTTATGGACAT
GCTGTTCTCCGTAAAACAGATCCTCGTTACACATGCCAACGTGAATTTGCTCTTAAACAT
TTACCTGATGATGTCCTCTTCAAACTTGTCAGCAACATTTACAAGGTCGTACCACCAATT
CTCACTGAATTGGGCAAGGTCAAGAACCCATGGCCAAATGTAGATGCTCACTCAGGCGTC
TTACTTCAATATTATGGACTCAAAGAGATGAACTACTACACTGTTTTATTTGGTGTATCA
CGTGCTCTTGGTGTTCTTGCTGGCTTGGTATGGGATCGTGCTCTTGGATTACCAATTGAG
CGACCTAAATCAATGTCAACTGAAGGATTAATGAAGGCAGTCGGATACAAAGCTTAAATC
CAAATATCTTAAACCTTAAAACATTTTTTCATATACAAATGAAGCATTAATTGAGTTCAA
TGAACCAATATCAAACGATTAACTTTTTTGACTGATTGTGAATTTTCAGTCAATATGATA
TGCAATAGTAGTTACTTTACCAAAAACAGTTTTCATTTTTACATACTTTCTTGTTACATT
ACATCTCTCTTTTTATAAAATTGAGACTTAAATCGGCGCTTTAACATTAAACATTTTATT
TGTTTTAGTTTCACCTGCATGACTCGAGATTATTTTCGAGTACAGTAACCCTCAACTTTA
TATTTTTCTTACCTCAATCAACACTATATATTGTATGTGTGATTGAAATTTTTAACTTAA
TTTATAAAAAAGGAAAGTATGAAAGGAAAACTGACCTCCTCCCCAAAAAATACGTGTGTA
GGAAAATTATTATATAAGATTACCTAGTAGAACCAACAGCAGCAAAGAAACACTTATTGC
AAAGAAAATAAATTTTACATCTCTACATTGTAGTAGTAATTTCAAATTAATGATAATAAT
GATAGAGAAGATAATAATTTAACTTTTAATTATAAAGGAACTTATTAAAAATTATTACTT
TGATTAAAAAGTGTAAAGTTTTGGATCAGGACATTATCTATTGGATCTATTTTATGTGAA
AGAATATTTAAATTTTCAATAAAATAAATTGTTGATGAGAATTTTCTTTTGACATAAA
>g4519.t17 Gene=g4519 Length=263
MDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDWSANFTRMLGYDNEEFTELMRLYLTIH
SDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLVWIQKLRSELGDN
ASEDKVKDFIWKTLKSGQVVPGYGHAVLRKTDPRYTCQREFALKHLPDDVLFKLVSNIYK
VVPPILTELGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLAGLVWDRAL
GLPIERPKSMSTEGLMKAVGYKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4519.t17 | Gene3D | G3DSA:1.10.580.10 | Citrate Synthase | 1 | 116 | 5.9E-49 |
| 13 | g4519.t17 | Gene3D | G3DSA:1.10.580.10 | Citrate Synthase | 187 | 248 | 1.8E-14 |
| 2 | g4519.t17 | PANTHER | PTHR11739:SF8 | CITRATE SYNTHASE, MITOCHONDRIAL | 1 | 260 | 1.9E-156 |
| 3 | g4519.t17 | PANTHER | PTHR11739 | CITRATE SYNTHASE | 1 | 260 | 1.9E-156 |
| 8 | g4519.t17 | PRINTS | PR00143 | Citrate synthase signature | 3 | 16 | 1.3E-54 |
| 6 | g4519.t17 | PRINTS | PR00143 | Citrate synthase signature | 52 | 67 | 1.3E-54 |
| 9 | g4519.t17 | PRINTS | PR00143 | Citrate synthase signature | 75 | 103 | 1.3E-54 |
| 5 | g4519.t17 | PRINTS | PR00143 | Citrate synthase signature | 135 | 155 | 1.3E-54 |
| 7 | g4519.t17 | PRINTS | PR00143 | Citrate synthase signature | 196 | 212 | 1.3E-54 |
| 4 | g4519.t17 | PRINTS | PR00143 | Citrate synthase signature | 217 | 231 | 1.3E-54 |
| 1 | g4519.t17 | Pfam | PF00285 | Citrate synthase, C-terminal domain | 1 | 248 | 2.3E-77 |
| 11 | g4519.t17 | ProSitePatterns | PS00480 | Citrate synthase signature. | 142 | 154 | - |
| 10 | g4519.t17 | SUPERFAMILY | SSF48256 | Citrate synthase | 1 | 257 | 8.37E-99 |
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.
