Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable citrate synthase 2, mitochondrial.

Parent gene

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.t15 TSS g4519.t15 2974301 2974301
chr_2 g4519 g4519.t15 isoform g4519.t15 2976222 2978258
chr_2 g4519 g4519.t15 exon g4519.t15.exon1 2976222 2976582
chr_2 g4519 g4519.t15 cds g4519.t15.CDS1 2976223 2976582
chr_2 g4519 g4519.t15 exon g4519.t15.exon2 2976650 2976876
chr_2 g4519 g4519.t15 cds g4519.t15.CDS2 2976650 2976876
chr_2 g4519 g4519.t15 exon g4519.t15.exon3 2976941 2978258
chr_2 g4519 g4519.t15 cds g4519.t15.CDS3 2976941 2977550
chr_2 g4519 g4519.t15 TTS g4519.t15 2978267 2978267

Sequences

>g4519.t15 Gene=g4519 Length=1906
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
AAGAATATTTAAATTTTCAATAAAATAAATTGTTGATGAGAATTTT

>g4519.t15 Gene=g4519 Length=398
MYGGMRGIKGLVYETSVLDPDEGIRFRGLSIPECQQVLPKAPGGSEPLPEGLFWLLITGD
VPNQQQVNWLSREWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALNHDSKYAKAYSE
GVHKSKYWEYVYEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDWSANFTRMLGYD
NEEFTELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQE
VLVWIQKLRSELGDNASEDKVKDFIWKTLKSGQVVPGYGHAVLRKTDPRYTCQREFALKH
LPDDVLFKLVSNIYKVVPPILTELGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVS
RALGVLAGLVWDRALGLPIERPKSMSTEGLMKAVGYKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4519.t15 CDD cd06105 ScCit1-2_like 1 392 0.0
11 g4519.t15 Gene3D G3DSA:1.10.580.10 Citrate Synthase 1 383 1.1E-197
12 g4519.t15 Gene3D G3DSA:1.10.230.10 - 237 351 1.1E-197
2 g4519.t15 PANTHER PTHR11739 CITRATE SYNTHASE 1 397 2.2E-236
3 g4519.t15 PANTHER PTHR11739:SF29 CITRATE SYNTHASE 1 397 2.2E-236
6 g4519.t15 PRINTS PR00143 Citrate synthase signature 138 151 7.4E-54
4 g4519.t15 PRINTS PR00143 Citrate synthase signature 187 202 7.4E-54
8 g4519.t15 PRINTS PR00143 Citrate synthase signature 210 238 7.4E-54
7 g4519.t15 PRINTS PR00143 Citrate synthase signature 270 290 7.4E-54
5 g4519.t15 PRINTS PR00143 Citrate synthase signature 331 347 7.4E-54
9 g4519.t15 PRINTS PR00143 Citrate synthase signature 352 366 7.4E-54
1 g4519.t15 Pfam PF00285 Citrate synthase, C-terminal domain 4 383 1.4E-104
14 g4519.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 351 -
15 g4519.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 352 371 -
13 g4519.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 372 398 -
17 g4519.t15 ProSitePatterns PS00480 Citrate synthase signature. 277 289 -
10 g4519.t15 SUPERFAMILY SSF48256 Citrate synthase 2 392 1.22E-142
18 g4519.t15 TIGRFAM TIGR01793 cit_synth_euk: citrate (Si)-synthase, eukaryotic 1 390 9.4E-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

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.

Raw TPM values