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.t9 TSS g4519.t9 2974301 2974301
chr_2 g4519 g4519.t9 isoform g4519.t9 2974357 2978267
chr_2 g4519 g4519.t9 exon g4519.t9.exon1 2974357 2974407
chr_2 g4519 g4519.t9 cds g4519.t9.CDS1 2974357 2974407
chr_2 g4519 g4519.t9 exon g4519.t9.exon2 2975488 2975649
chr_2 g4519 g4519.t9 cds g4519.t9.CDS2 2975488 2975649
chr_2 g4519 g4519.t9 exon g4519.t9.exon3 2976289 2976582
chr_2 g4519 g4519.t9 cds g4519.t9.CDS3 2976289 2976582
chr_2 g4519 g4519.t9 exon g4519.t9.exon4 2976650 2976876
chr_2 g4519 g4519.t9 cds g4519.t9.CDS4 2976650 2976876
chr_2 g4519 g4519.t9 exon g4519.t9.exon5 2976941 2978267
chr_2 g4519 g4519.t9 cds g4519.t9.CDS5 2976941 2977550
chr_2 g4519 g4519.t9 TTS g4519.t9 2978267 2978267

Sequences

>g4519.t9 Gene=g4519 Length=2061
ATGGCTTTATTCAGAATTTCATCTACTAAATGCCTAACTGAGGTTCATCAGAGATTCTTG
CCAGCGATCATAACATGTGTAAGAAACATCTCGGCAGATAGCACCGATTTGAAAGCAATT
TTAGCAGACAAAATTCCAAAGGAACAGGAACGTGTGAAGAACTTCCGCAAAGCTCATGGC
GCAACAAAAGTTGGCGAAGTTACAATTGATATGGGAATTCGTTTCCGTGGATTATCAATT
CCTGAATGCCAGCAAGTTTTGCCAAAAGCTCCAGGCGGTTCTGAGCCATTGCCAGAGGGT
CTTTTCTGGCTTCTCATTACCGGTGATGTTCCAAATCAACAGCAAGTCAATTGGTTGTCA
CGTGAATGGTCAAATCGTGCTGCACTTCCGGGCCACGTTGTAACAATGCTCAACAACTTT
CCAACAACTCTCCATCCAATGTCACAATTTTCAGCTGCTATCACAGCATTGAATCATGAC
AGCAAATACGCAAAAGCATATTCAGAAGGTGTACACAAAAGCAAATACTGGGAATATGTC
TACGAAGATAGCATGGACTTGATTGCTAAATTGCCAGTTGTAGCTGCAACAATTTATCGC
AATACTTATCGTGATGGAAAGGGTATTGGAGCAATCGATTCAAAGCTTGATTGGTCTGCC
AATTTCACTCGTATGCTCGGTTATGATAACGAAGAATTCACCGAATTAATGCGTTTATAT
CTCACCATTCACAGTGATCATGAGGGTGGCAATGTTAGCGCACACACAGTTCATCTTGTT
GGATCAGCACTTAGTGATCCATATCTCTCATTCGCTGCCGGCATGAATGGTTTGGCTGGT
CCACTTCACGGTTTAGCTAATCAAGAAGTATTGGTTTGGATTCAAAAATTACGTAGTGAA
CTCGGTGATAATGCATCAGAAGATAAAGTTAAGGACTTTATCTGGAAGACACTTAAATCA
GGTCAAGTTGTTCCAGGTTATGGACATGCTGTTCTCCGTAAAACAGATCCTCGTTACACA
TGCCAACGTGAATTTGCTCTTAAACATTTACCTGATGATGTCCTCTTCAAACTTGTCAGC
AACATTTACAAGGTCGTACCACCAATTCTCACTGAATTGGGCAAGGTCAAGAACCCATGG
CCAAATGTAGATGCTCACTCAGGCGTCTTACTTCAATATTATGGACTCAAAGAGATGAAC
TACTACACTGTTTTATTTGGTGTATCACGTGCTCTTGGTGTTCTTGCTGGCTTGGTATGG
GATCGTGCTCTTGGATTACCAATTGAGCGACCTAAATCAATGTCAACTGAAGGATTAATG
AAGGCAGTCGGATACAAAGCTTAAATCCAAATATCTTAAACCTTAAAACATTTTTTCATA
TACAAATGAAGCATTAATTGAGTTCAATGAACCAATATCAAACGATTAACTTTTTTGACT
GATTGTGAATTTTCAGTCAATATGATATGCAATAGTAGTTACTTTACCAAAAACAGTTTT
CATTTTTACATACTTTCTTGTTACATTACATCTCTCTTTTTATAAAATTGAGACTTAAAT
CGGCGCTTTAACATTAAACATTTTATTTGTTTTAGTTTCACCTGCATGACTCGAGATTAT
TTTCGAGTACAGTAACCCTCAACTTTATATTTTTCTTACCTCAATCAACACTATATATTG
TATGTGTGATTGAAATTTTTAACTTAATTTATAAAAAAGGAAAGTATGAAAGGAAAACTG
ACCTCCTCCCCAAAAAATACGTGTGTAGGAAAATTATTATATAAGATTACCTAGTAGAAC
CAACAGCAGCAAAGAAACACTTATTGCAAAGAAAATAAATTTTACATCTCTACATTGTAG
TAGTAATTTCAAATTAATGATAATAATGATAGAGAAGATAATAATTTAACTTTTAATTAT
AAAGGAACTTATTAAAAATTATTACTTTGATTAAAAAGTGTAAAGTTTTGGATCAGGACA
TTATCTATTGGATCTATTTTATGTGAAAGAATATTTAAATTTTCAATAAAATAAATTGTT
GATGAGAATTTTCTTTTGACA

>g4519.t9 Gene=g4519 Length=447
MALFRISSTKCLTEVHQRFLPAIITCVRNISADSTDLKAILADKIPKEQERVKNFRKAHG
ATKVGEVTIDMGIRFRGLSIPECQQVLPKAPGGSEPLPEGLFWLLITGDVPNQQQVNWLS
REWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALNHDSKYAKAYSEGVHKSKYWEYV
YEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDWSANFTRMLGYDNEEFTELMRLY
LTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGLAGPLHGLANQEVLVWIQKLRSE
LGDNASEDKVKDFIWKTLKSGQVVPGYGHAVLRKTDPRYTCQREFALKHLPDDVLFKLVS
NIYKVVPPILTELGKVKNPWPNVDAHSGVLLQYYGLKEMNYYTVLFGVSRALGVLAGLVW
DRALGLPIERPKSMSTEGLMKAVGYKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4519.t9 CDD cd06105 ScCit1-2_like 37 441 0.0
11 g4519.t9 Gene3D G3DSA:1.10.580.10 Citrate Synthase 71 432 9.8E-187
12 g4519.t9 Gene3D G3DSA:1.10.230.10 - 286 400 9.8E-187
2 g4519.t9 PANTHER PTHR11739 CITRATE SYNTHASE 70 446 9.8E-227
3 g4519.t9 PANTHER PTHR11739:SF29 CITRATE SYNTHASE 70 446 9.8E-227
4 g4519.t9 PRINTS PR00143 Citrate synthase signature 187 200 1.2E-53
5 g4519.t9 PRINTS PR00143 Citrate synthase signature 236 251 1.2E-53
8 g4519.t9 PRINTS PR00143 Citrate synthase signature 259 287 1.2E-53
7 g4519.t9 PRINTS PR00143 Citrate synthase signature 319 339 1.2E-53
6 g4519.t9 PRINTS PR00143 Citrate synthase signature 380 396 1.2E-53
9 g4519.t9 PRINTS PR00143 Citrate synthase signature 401 415 1.2E-53
1 g4519.t9 Pfam PF00285 Citrate synthase, C-terminal domain 62 432 5.5E-103
14 g4519.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 400 -
15 g4519.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 401 420 -
13 g4519.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 421 447 -
17 g4519.t9 ProSitePatterns PS00480 Citrate synthase signature. 326 338 -
10 g4519.t9 SUPERFAMILY SSF48256 Citrate synthase 34 441 2.62E-139
18 g4519.t9 TIGRFAM TIGR01793 cit_synth_euk: citrate (Si)-synthase, eukaryotic 72 439 9.4E-213

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