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.t16 isoform g4519.t16 2976231 2977550
chr_2 g4519 g4519.t16 exon g4519.t16.exon1 2976231 2976582
chr_2 g4519 g4519.t16 exon g4519.t16.exon2 2976650 2976854
chr_2 g4519 g4519.t16 exon g4519.t16.exon3 2976941 2977550
chr_2 g4519 g4519.t16 cds g4519.t16.CDS1 2977029 2977550
chr_2 g4519 g4519.t16 TTS g4519.t16 2978267 2978267
chr_2 g4519 g4519.t16 TSS g4519.t16 NA NA

Sequences

>g4519.t16 Gene=g4519 Length=1167
TGGCATGCGTGGCATTAAAGGTCTTGTCTATGAGACATCTGTCTTGGATCCAGATGAGGG
AATTCGTTTCCGTGGATTATCAATTCCTGAATGCCAGCAAGTTTTGCCAAAAGCTCCAGG
CGGTTCTGAGCCATTGCCAGAGGGTCTTTTCTGGCTTCTCATTACCGGTGATGTTCCAAA
TCAACAGCAAGTCAATTGGTTGTCACGTGAATGGTCAAATCGTGCTGCACTTCCGGGCCA
CGTTGTAACAATGCTCAACAACTTTCCAACAACTCTCCATCCAATGTCACAATTTTCAGC
TGCTATCACAGCATTGAATCATGACAGCAAATACGCAAAAGCATATTCAGAAGGTGTACA
CAAAAGCAAATACTGGGAATATGTCTACGAAGATAGCATGGACTTGATTGCTAAATTGCC
AGTTGTAGCTGCAACAATTTATCGCAATACTTATCGTGATGGAAAGGGTATTGGAGCAAT
CGATTCAAAGCTTGATTGGTCTGCCAATTTCACTCGTATGCTCGGTTATGATAACGAAGA
ATTCACCGAATTAATGCTGATCATGAGGGTGGCAATGTTAGCGCACACACAGTTCATCTT
GTTGGATCAGCACTTAGTGATCCATATCTCTCATTCGCTGCCGGCATGAATGGTTTGGCT
GGTCCACTTCACGGTTTAGCTAATCAAGAAGTATTGGTTTGGATTCAAAAATTACGTAGT
GAACTCGGTGATAATGCATCAGAAGATAAAGTTAAGGACTTTATCTGGAAGACACTTAAA
TCAGGTCAAGTTGTTCCAGGTTATGGACATGCTGTTCTCCGTAAAACAGATCCTCGTTAC
ACATGCCAACGTGAATTTGCTCTTAAACATTTACCTGATGATGTCCTCTTCAAACTTGTC
AGCAACATTTACAAGGTCGTACCACCAATTCTCACTGAATTGGGCAAGGTCAAGAACCCA
TGGCCAAATGTAGATGCTCACTCAGGCGTCTTACTTCAATATTATGGACTCAAAGAGATG
AACTACTACACTGTTTTATTTGGTGTATCACGTGCTCTTGGTGTTCTTGCTGGCTTGGTA
TGGGATCGTGCTCTTGGATTACCAATTGAGCGACCTAAATCAATGTCAACTGAAGGATTA
ATGAAGGCAGTCGGATACAAAGCTTAA

>g4519.t16 Gene=g4519 Length=173
MNGLAGPLHGLANQEVLVWIQKLRSELGDNASEDKVKDFIWKTLKSGQVVPGYGHAVLRK
TDPRYTCQREFALKHLPDDVLFKLVSNIYKVVPPILTELGKVKNPWPNVDAHSGVLLQYY
GLKEMNYYTVLFGVSRALGVLAGLVWDRALGLPIERPKSMSTEGLMKAVGYKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4519.t16 Gene3D G3DSA:1.10.230.10 - 12 126 2.4E-42
2 g4519.t16 PANTHER PTHR11739:SF8 CITRATE SYNTHASE, MITOCHONDRIAL 1 170 3.9E-99
3 g4519.t16 PANTHER PTHR11739 CITRATE SYNTHASE 1 170 3.9E-99
6 g4519.t16 PRINTS PR00143 Citrate synthase signature 45 65 1.3E-23
5 g4519.t16 PRINTS PR00143 Citrate synthase signature 106 122 1.3E-23
4 g4519.t16 PRINTS PR00143 Citrate synthase signature 127 141 1.3E-23
1 g4519.t16 Pfam PF00285 Citrate synthase, C-terminal domain 1 158 1.7E-43
8 g4519.t16 ProSitePatterns PS00480 Citrate synthase signature. 52 64 -
7 g4519.t16 SUPERFAMILY SSF48256 Citrate synthase 2 165 9.55E-62

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:0046912 acyltransferase, acyl groups converted into alkyl on transfer MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed