General information for g4519.t10
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.t10 | TSS | g4519.t10 | 2974301 | 2974301 |
| chr_2 | g4519 | g4519.t10 | isoform | g4519.t10 | 2974357 | 2978267 |
| chr_2 | g4519 | g4519.t10 | exon | g4519.t10.exon1 | 2974357 | 2974407 |
| chr_2 | g4519 | g4519.t10 | exon | g4519.t10.exon2 | 2975460 | 2975649 |
| chr_2 | g4519 | g4519.t10 | cds | g4519.t10.CDS1 | 2975647 | 2975649 |
| chr_2 | g4519 | g4519.t10 | exon | g4519.t10.exon3 | 2976223 | 2976582 |
| chr_2 | g4519 | g4519.t10 | cds | g4519.t10.CDS2 | 2976223 | 2976582 |
| chr_2 | g4519 | g4519.t10 | exon | g4519.t10.exon4 | 2976650 | 2976876 |
| chr_2 | g4519 | g4519.t10 | cds | g4519.t10.CDS3 | 2976650 | 2976876 |
| chr_2 | g4519 | g4519.t10 | exon | g4519.t10.exon5 | 2976941 | 2978267 |
| chr_2 | g4519 | g4519.t10 | cds | g4519.t10.CDS4 | 2976941 | 2977550 |
| chr_2 | g4519 | g4519.t10 | TTS | g4519.t10 | 2978267 | 2978267 |
Sequences
>g4519.t10 Gene=g4519 Length=2155
ATGGCTTTATTCAGAATTTCATCTACTAAATGCCTAACTGAGGTTCATCAGTTATATTTT
TTATTTGATGAATAAATAGAGATTCTTGCCAGCGATCATAACATGTGTAAGAAACATCTC
GGCAGATAGCACCGATTTGAAAGCAATTTTAGCAGACAAAATTCCAAAGGAACAGGAACG
TGTGAAGAACTTCCGCAAAGCTCATGGCGCAACAAAAGTTGGCGAAGTTACAATTGATAT
GATGTATGGTGGCATGCGTGGCATTAAAGGTCTTGTCTATGAGACATCTGTCTTGGATCC
AGATGAGGGAATTCGTTTCCGTGGATTATCAATTCCTGAATGCCAGCAAGTTTTGCCAAA
AGCTCCAGGCGGTTCTGAGCCATTGCCAGAGGGTCTTTTCTGGCTTCTCATTACCGGTGA
TGTTCCAAATCAACAGCAAGTCAATTGGTTGTCACGTGAATGGTCAAATCGTGCTGCACT
TCCGGGCCACGTTGTAACAATGCTCAACAACTTTCCAACAACTCTCCATCCAATGTCACA
ATTTTCAGCTGCTATCACAGCATTGAATCATGACAGCAAATACGCAAAAGCATATTCAGA
AGGTGTACACAAAAGCAAATACTGGGAATATGTCTACGAAGATAGCATGGACTTGATTGC
TAAATTGCCAGTTGTAGCTGCAACAATTTATCGCAATACTTATCGTGATGGAAAGGGTAT
TGGAGCAATCGATTCAAAGCTTGATTGGTCTGCCAATTTCACTCGTATGCTCGGTTATGA
TAACGAAGAATTCACCGAATTAATGCGTTTATATCTCACCATTCACAGTGATCATGAGGG
TGGCAATGTTAGCGCACACACAGTTCATCTTGTTGGATCAGCACTTAGTGATCCATATCT
CTCATTCGCTGCCGGCATGAATGGTTTGGCTGGTCCACTTCACGGTTTAGCTAATCAAGA
AGTATTGGTTTGGATTCAAAAATTACGTAGTGAACTCGGTGATAATGCATCAGAAGATAA
AGTTAAGGACTTTATCTGGAAGACACTTAAATCAGGTCAAGTTGTTCCAGGTTATGGACA
TGCTGTTCTCCGTAAAACAGATCCTCGTTACACATGCCAACGTGAATTTGCTCTTAAACA
TTTACCTGATGATGTCCTCTTCAAACTTGTCAGCAACATTTACAAGGTCGTACCACCAAT
TCTCACTGAATTGGGCAAGGTCAAGAACCCATGGCCAAATGTAGATGCTCACTCAGGCGT
CTTACTTCAATATTATGGACTCAAAGAGATGAACTACTACACTGTTTTATTTGGTGTATC
ACGTGCTCTTGGTGTTCTTGCTGGCTTGGTATGGGATCGTGCTCTTGGATTACCAATTGA
GCGACCTAAATCAATGTCAACTGAAGGATTAATGAAGGCAGTCGGATACAAAGCTTAAAT
CCAAATATCTTAAACCTTAAAACATTTTTTCATATACAAATGAAGCATTAATTGAGTTCA
ATGAACCAATATCAAACGATTAACTTTTTTGACTGATTGTGAATTTTCAGTCAATATGAT
ATGCAATAGTAGTTACTTTACCAAAAACAGTTTTCATTTTTACATACTTTCTTGTTACAT
TACATCTCTCTTTTTATAAAATTGAGACTTAAATCGGCGCTTTAACATTAAACATTTTAT
TTGTTTTAGTTTCACCTGCATGACTCGAGATTATTTTCGAGTACAGTAACCCTCAACTTT
ATATTTTTCTTACCTCAATCAACACTATATATTGTATGTGTGATTGAAATTTTTAACTTA
ATTTATAAAAAAGGAAAGTATGAAAGGAAAACTGACCTCCTCCCCAAAAAATACGTGTGT
AGGAAAATTATTATATAAGATTACCTAGTAGAACCAACAGCAGCAAAGAAACACTTATTG
CAAAGAAAATAAATTTTACATCTCTACATTGTAGTAGTAATTTCAAATTAATGATAATAA
TGATAGAGAAGATAATAATTTAACTTTTAATTATAAAGGAACTTATTAAAAATTATTACT
TTGATTAAAAAGTGTAAAGTTTTGGATCAGGACATTATCTATTGGATCTATTTTATGTGA
AAGAATATTTAAATTTTCAATAAAATAAATTGTTGATGAGAATTTTCTTTTGACA
>g4519.t10 Gene=g4519 Length=399
MMYGGMRGIKGLVYETSVLDPDEGIRFRGLSIPECQQVLPKAPGGSEPLPEGLFWLLITG
DVPNQQQVNWLSREWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALNHDSKYAKAYS
EGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDWSANFTRMLGY
DNEEFTELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQ
EVLVWIQKLRSELGDNASEDKVKDFIWKTLKSGQVVPGYGHAVLRKTDPRYTCQREFALK
HLPDDVLFKLVSNIYKVVPPILTELGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGV
SRALGVLAGLVWDRALGLPIERPKSMSTEGLMKAVGYKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4519.t10 | CDD | cd06105 | ScCit1-2_like | 1 | 393 | 0.0 |
| 11 | g4519.t10 | Gene3D | G3DSA:1.10.580.10 | Citrate Synthase | 1 | 384 | 4.3E-198 |
| 12 | g4519.t10 | Gene3D | G3DSA:1.10.230.10 | - | 238 | 352 | 4.3E-198 |
| 2 | g4519.t10 | PANTHER | PTHR11739 | CITRATE SYNTHASE | 1 | 398 | 3.4E-237 |
| 3 | g4519.t10 | PANTHER | PTHR11739:SF29 | CITRATE SYNTHASE | 1 | 398 | 3.4E-237 |
| 8 | g4519.t10 | PRINTS | PR00143 | Citrate synthase signature | 139 | 152 | 7.5E-54 |
| 6 | g4519.t10 | PRINTS | PR00143 | Citrate synthase signature | 188 | 203 | 7.5E-54 |
| 7 | g4519.t10 | PRINTS | PR00143 | Citrate synthase signature | 211 | 239 | 7.5E-54 |
| 5 | g4519.t10 | PRINTS | PR00143 | Citrate synthase signature | 271 | 291 | 7.5E-54 |
| 4 | g4519.t10 | PRINTS | PR00143 | Citrate synthase signature | 332 | 348 | 7.5E-54 |
| 9 | g4519.t10 | PRINTS | PR00143 | Citrate synthase signature | 353 | 367 | 7.5E-54 |
| 1 | g4519.t10 | Pfam | PF00285 | Citrate synthase, C-terminal domain | 5 | 384 | 1.4E-104 |
| 13 | g4519.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 352 | - |
| 15 | g4519.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 353 | 372 | - |
| 14 | g4519.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 373 | 399 | - |
| 17 | g4519.t10 | ProSitePatterns | PS00480 | Citrate synthase signature. | 278 | 290 | - |
| 10 | g4519.t10 | SUPERFAMILY | SSF48256 | Citrate synthase | 1 | 393 | 6.02E-143 |
| 18 | g4519.t10 | TIGRFAM | TIGR01793 | cit_synth_euk: citrate (Si)-synthase, eukaryotic | 1 | 391 | 2.6E-226 |
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:0006101 | citrate metabolic process | BP |
| GO:0046912 | acyltransferase, acyl groups converted into alkyl on transfer | MF |
| GO:0004108 | citrate (Si)-synthase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01647 (citrate synthase)
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.
