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.t1 TSS g4519.t1 2974301 2974301
chr_2 g4519 g4519.t1 isoform g4519.t1 2974357 2977550
chr_2 g4519 g4519.t1 exon g4519.t1.exon1 2974357 2974407
chr_2 g4519 g4519.t1 cds g4519.t1.CDS1 2974357 2974407
chr_2 g4519 g4519.t1 exon g4519.t1.exon2 2975488 2975649
chr_2 g4519 g4519.t1 cds g4519.t1.CDS2 2975488 2975649
chr_2 g4519 g4519.t1 exon g4519.t1.exon3 2976223 2976582
chr_2 g4519 g4519.t1 cds g4519.t1.CDS3 2976223 2976582
chr_2 g4519 g4519.t1 exon g4519.t1.exon4 2976650 2976876
chr_2 g4519 g4519.t1 cds g4519.t1.CDS4 2976650 2976876
chr_2 g4519 g4519.t1 exon g4519.t1.exon5 2976941 2977550
chr_2 g4519 g4519.t1 cds g4519.t1.CDS5 2976941 2977550
chr_2 g4519 g4519.t1 TTS g4519.t1 2978267 2978267

Sequences

>g4519.t1 Gene=g4519 Length=1410
ATGGCTTTATTCAGAATTTCATCTACTAAATGCCTAACTGAGGTTCATCAGAGATTCTTG
CCAGCGATCATAACATGTGTAAGAAACATCTCGGCAGATAGCACCGATTTGAAAGCAATT
TTAGCAGACAAAATTCCAAAGGAACAGGAACGTGTGAAGAACTTCCGCAAAGCTCATGGC
GCAACAAAAGTTGGCGAAGTTACAATTGATATGATGTATGGTGGCATGCGTGGCATTAAA
GGTCTTGTCTATGAGACATCTGTCTTGGATCCAGATGAGGGAATTCGTTTCCGTGGATTA
TCAATTCCTGAATGCCAGCAAGTTTTGCCAAAAGCTCCAGGCGGTTCTGAGCCATTGCCA
GAGGGTCTTTTCTGGCTTCTCATTACCGGTGATGTTCCAAATCAACAGCAAGTCAATTGG
TTGTCACGTGAATGGTCAAATCGTGCTGCACTTCCGGGCCACGTTGTAACAATGCTCAAC
AACTTTCCAACAACTCTCCATCCAATGTCACAATTTTCAGCTGCTATCACAGCATTGAAT
CATGACAGCAAATACGCAAAAGCATATTCAGAAGGTGTACACAAAAGCAAATACTGGGAA
TATGTCTACGAAGATAGCATGGACTTGATTGCTAAATTGCCAGTTGTAGCTGCAACAATT
TATCGCAATACTTATCGTGATGGAAAGGGTATTGGAGCAATCGATTCAAAGCTTGATTGG
TCTGCCAATTTCACTCGTATGCTCGGTTATGATAACGAAGAATTCACCGAATTAATGCGT
TTATATCTCACCATTCACAGTGATCATGAGGGTGGCAATGTTAGCGCACACACAGTTCAT
CTTGTTGGATCAGCACTTAGTGATCCATATCTCTCATTCGCTGCCGGCATGAATGGTTTG
GCTGGTCCACTTCACGGTTTAGCTAATCAAGAAGTATTGGTTTGGATTCAAAAATTACGT
AGTGAACTCGGTGATAATGCATCAGAAGATAAAGTTAAGGACTTTATCTGGAAGACACTT
AAATCAGGTCAAGTTGTTCCAGGTTATGGACATGCTGTTCTCCGTAAAACAGATCCTCGT
TACACATGCCAACGTGAATTTGCTCTTAAACATTTACCTGATGATGTCCTCTTCAAACTT
GTCAGCAACATTTACAAGGTCGTACCACCAATTCTCACTGAATTGGGCAAGGTCAAGAAC
CCATGGCCAAATGTAGATGCTCACTCAGGCGTCTTACTTCAATATTATGGACTCAAAGAG
ATGAACTACTACACTGTTTTATTTGGTGTATCACGTGCTCTTGGTGTTCTTGCTGGCTTG
GTATGGGATCGTGCTCTTGGATTACCAATTGAGCGACCTAAATCAATGTCAACTGAAGGA
TTAATGAAGGCAGTCGGATACAAAGCTTAA

>g4519.t1 Gene=g4519 Length=469
MALFRISSTKCLTEVHQRFLPAIITCVRNISADSTDLKAILADKIPKEQERVKNFRKAHG
ATKVGEVTIDMMYGGMRGIKGLVYETSVLDPDEGIRFRGLSIPECQQVLPKAPGGSEPLP
EGLFWLLITGDVPNQQQVNWLSREWSNRAALPGHVVTMLNNFPTTLHPMSQFSAAITALN
HDSKYAKAYSEGVHKSKYWEYVYEDSMDLIAKLPVVAATIYRNTYRDGKGIGAIDSKLDW
SANFTRMLGYDNEEFTELMRLYLTIHSDHEGGNVSAHTVHLVGSALSDPYLSFAAGMNGL
AGPLHGLANQEVLVWIQKLRSELGDNASEDKVKDFIWKTLKSGQVVPGYGHAVLRKTDPR
YTCQREFALKHLPDDVLFKLVSNIYKVVPPILTELGKVKNPWPNVDAHSGVLLQYYGLKE
MNYYTVLFGVSRALGVLAGLVWDRALGLPIERPKSMSTEGLMKAVGYKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4519.t1 CDD cd06105 ScCit1-2_like 37 463 0.0
11 g4519.t1 Gene3D G3DSA:1.10.580.10 Citrate Synthase 41 454 2.6E-210
12 g4519.t1 Gene3D G3DSA:1.10.230.10 - 308 422 2.6E-210
2 g4519.t1 PANTHER PTHR11739 CITRATE SYNTHASE 45 468 9.3E-250
3 g4519.t1 PANTHER PTHR11739:SF29 CITRATE SYNTHASE 45 468 9.3E-250
4 g4519.t1 PRINTS PR00143 Citrate synthase signature 209 222 1.5E-53
5 g4519.t1 PRINTS PR00143 Citrate synthase signature 258 273 1.5E-53
6 g4519.t1 PRINTS PR00143 Citrate synthase signature 281 309 1.5E-53
9 g4519.t1 PRINTS PR00143 Citrate synthase signature 341 361 1.5E-53
7 g4519.t1 PRINTS PR00143 Citrate synthase signature 402 418 1.5E-53
8 g4519.t1 PRINTS PR00143 Citrate synthase signature 423 437 1.5E-53
1 g4519.t1 Pfam PF00285 Citrate synthase, C-terminal domain 75 454 2.5E-104
14 g4519.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 422 -
15 g4519.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 423 442 -
13 g4519.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 443 469 -
17 g4519.t1 ProSitePatterns PS00480 Citrate synthase signature. 348 360 -
10 g4519.t1 SUPERFAMILY SSF48256 Citrate synthase 34 463 3.4E-150
18 g4519.t1 TIGRFAM TIGR01793 cit_synth_euk: citrate (Si)-synthase, eukaryotic 35 461 7.5E-242

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