Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable citrate synthase 1, 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.t7 TSS g4519.t7 2974301 2974301
chr_2 g4519 g4519.t7 isoform g4519.t7 2974357 2977550
chr_2 g4519 g4519.t7 exon g4519.t7.exon1 2974357 2974407
chr_2 g4519 g4519.t7 exon g4519.t7.exon2 2975464 2975649
chr_2 g4519 g4519.t7 cds g4519.t7.CDS1 2975647 2975649
chr_2 g4519 g4519.t7 exon g4519.t7.exon3 2976223 2976582
chr_2 g4519 g4519.t7 cds g4519.t7.CDS2 2976223 2976582
chr_2 g4519 g4519.t7 exon g4519.t7.exon4 2976650 2976876
chr_2 g4519 g4519.t7 cds g4519.t7.CDS3 2976650 2976876
chr_2 g4519 g4519.t7 exon g4519.t7.exon5 2976941 2977550
chr_2 g4519 g4519.t7 cds g4519.t7.CDS4 2976941 2977550
chr_2 g4519 g4519.t7 TTS g4519.t7 2978267 2978267

Sequences

>g4519.t7 Gene=g4519 Length=1434
ATGGCTTTATTCAGAATTTCATCTACTAAATGCCTAACTGAGGTTCATCAGATTTTTTAT
TTGATGAATAAATAGAGATTCTTGCCAGCGATCATAACATGTGTAAGAAACATCTCGGCA
GATAGCACCGATTTGAAAGCAATTTTAGCAGACAAAATTCCAAAGGAACAGGAACGTGTG
AAGAACTTCCGCAAAGCTCATGGCGCAACAAAAGTTGGCGAAGTTACAATTGATATGATG
TATGGTGGCATGCGTGGCATTAAAGGTCTTGTCTATGAGACATCTGTCTTGGATCCAGAT
GAGGGAATTCGTTTCCGTGGATTATCAATTCCTGAATGCCAGCAAGTTTTGCCAAAAGCT
CCAGGCGGTTCTGAGCCATTGCCAGAGGGTCTTTTCTGGCTTCTCATTACCGGTGATGTT
CCAAATCAACAGCAAGTCAATTGGTTGTCACGTGAATGGTCAAATCGTGCTGCACTTCCG
GGCCACGTTGTAACAATGCTCAACAACTTTCCAACAACTCTCCATCCAATGTCACAATTT
TCAGCTGCTATCACAGCATTGAATCATGACAGCAAATACGCAAAAGCATATTCAGAAGGT
GTACACAAAAGCAAATACTGGGAATATGTCTACGAAGATAGCATGGACTTGATTGCTAAA
TTGCCAGTTGTAGCTGCAACAATTTATCGCAATACTTATCGTGATGGAAAGGGTATTGGA
GCAATCGATTCAAAGCTTGATTGGTCTGCCAATTTCACTCGTATGCTCGGTTATGATAAC
GAAGAATTCACCGAATTAATGCGTTTATATCTCACCATTCACAGTGATCATGAGGGTGGC
AATGTTAGCGCACACACAGTTCATCTTGTTGGATCAGCACTTAGTGATCCATATCTCTCA
TTCGCTGCCGGCATGAATGGTTTGGCTGGTCCACTTCACGGTTTAGCTAATCAAGAAGTA
TTGGTTTGGATTCAAAAATTACGTAGTGAACTCGGTGATAATGCATCAGAAGATAAAGTT
AAGGACTTTATCTGGAAGACACTTAAATCAGGTCAAGTTGTTCCAGGTTATGGACATGCT
GTTCTCCGTAAAACAGATCCTCGTTACACATGCCAACGTGAATTTGCTCTTAAACATTTA
CCTGATGATGTCCTCTTCAAACTTGTCAGCAACATTTACAAGGTCGTACCACCAATTCTC
ACTGAATTGGGCAAGGTCAAGAACCCATGGCCAAATGTAGATGCTCACTCAGGCGTCTTA
CTTCAATATTATGGACTCAAAGAGATGAACTACTACACTGTTTTATTTGGTGTATCACGT
GCTCTTGGTGTTCTTGCTGGCTTGGTATGGGATCGTGCTCTTGGATTACCAATTGAGCGA
CCTAAATCAATGTCAACTGAAGGATTAATGAAGGCAGTCGGATACAAAGCTTAA

>g4519.t7 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.t7 CDD cd06105 ScCit1-2_like 1 393 0.0
11 g4519.t7 Gene3D G3DSA:1.10.580.10 Citrate Synthase 1 384 4.3E-198
12 g4519.t7 Gene3D G3DSA:1.10.230.10 - 238 352 4.3E-198
2 g4519.t7 PANTHER PTHR11739 CITRATE SYNTHASE 1 398 3.4E-237
3 g4519.t7 PANTHER PTHR11739:SF29 CITRATE SYNTHASE 1 398 3.4E-237
8 g4519.t7 PRINTS PR00143 Citrate synthase signature 139 152 7.5E-54
6 g4519.t7 PRINTS PR00143 Citrate synthase signature 188 203 7.5E-54
7 g4519.t7 PRINTS PR00143 Citrate synthase signature 211 239 7.5E-54
5 g4519.t7 PRINTS PR00143 Citrate synthase signature 271 291 7.5E-54
4 g4519.t7 PRINTS PR00143 Citrate synthase signature 332 348 7.5E-54
9 g4519.t7 PRINTS PR00143 Citrate synthase signature 353 367 7.5E-54
1 g4519.t7 Pfam PF00285 Citrate synthase, C-terminal domain 5 384 1.4E-104
13 g4519.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 352 -
15 g4519.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 353 372 -
14 g4519.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 373 399 -
17 g4519.t7 ProSitePatterns PS00480 Citrate synthase signature. 278 290 -
10 g4519.t7 SUPERFAMILY SSF48256 Citrate synthase 1 393 6.02E-143
18 g4519.t7 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

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