Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP-citrate synthase.

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 g4512 g4512.t6 TTS g4512.t6 2949079 2949079
chr_2 g4512 g4512.t6 isoform g4512.t6 2949692 2950818
chr_2 g4512 g4512.t6 exon g4512.t6.exon1 2949692 2950019
chr_2 g4512 g4512.t6 cds g4512.t6.CDS1 2949693 2950019
chr_2 g4512 g4512.t6 exon g4512.t6.exon2 2950076 2950818
chr_2 g4512 g4512.t6 cds g4512.t6.CDS2 2950076 2950777
chr_2 g4512 g4512.t6 TSS g4512.t6 NA NA

Sequences

>g4512.t6 Gene=g4512 Length=1071
GTGTTGCAATTGGTGGTGATCGTTATCCCGGAACAACTTTTATGGATCATATCATGCGTT
ATCAAAATGATGATGGTGCAAAATTGATTGTTGTTCTTGGTGAAGTTGGTGGAGTTGAGG
AATATGAAATTTGTGCGGCTTTAAAAGATGGAAGAATTACAAAGCCATTGATTGCATGGT
GCATTGGAACATGTGCTGGAATGTTTACATCTGAAGTTCAATTCGGTCATGCTGGTTCAT
GCGCTCAATCAGATATGGAAACAGCTTCAGCTAAAAATAAGGCATTACGTGATGCAGGAG
CACATGTACCTGATTCTTTTGATACTCTTGGAGATTTAATTGCTCACGTTTATGAGGATA
TGGTACAAAGTGGACAAATTGTTCCCGCCGAAGAAGTTCCACCACCGACCGTTCCTATGG
ATTATAATTGGGCACGCGAGTTGGGATTGATTCGTAAGCCAGCCTCATTCATGACATCGA
TTTGTGATGAACGTGGACAAGAATTGTTGTATGCTGGAATGCCAATCAGTGAAGTTTTGA
CAAAAGATGTCGGTATTGGCGGTGTTGTTTCACTCTTATGGTTCCAACGTTGTTTACCAC
CATACGTTTGCAAATTCTTTGAGATGTGTTTAATGGTAACTGCAGATCACGGACCAGCCG
TCAGTGGAGCACACAATACAATTGTCTGTGCTCGTGCTGGAAAAGACCTTGTATCATCAC
TCGTGTCAGGATTGTTGACTATTGGTGACCGTTTTGGTGGGGCTCTTGATGGCGCAGCAA
AACAATTTTCTGAAGCATATGATTCGAATATGCATCCAATGGACTTTGTCAACTCAATGC
GTAAAAAGGGTCAACTTATCATGGGTATAGGTCATCGTGTAAAATCAATCAACAATCCTG
ATATTCGTGTTAAAATTATCAAAGAGTTTGTGCTCGAAAACTTCCCAGCTAAGCCACTTT
TGGAATATGCATTGGAAGTTGAAAAGATTACTACAAGTAAAAAGCCAAACTTGATTTTGA
ATGTCGACGGTGTCATTGCAACATGCTTCGTCGATATGTTGAGAAATTGTG

>g4512.t6 Gene=g4512 Length=343
MDHIMRYQNDDGAKLIVVLGEVGGVEEYEICAALKDGRITKPLIAWCIGTCAGMFTSEVQ
FGHAGSCAQSDMETASAKNKALRDAGAHVPDSFDTLGDLIAHVYEDMVQSGQIVPAEEVP
PPTVPMDYNWARELGLIRKPASFMTSICDERGQELLYAGMPISEVLTKDVGIGGVVSLLW
FQRCLPPYVCKFFEMCLMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTIGDRFGG
ALDGAAKQFSEAYDSNMHPMDFVNSMRKKGQLIMGIGHRVKSINNPDIRVKIIKEFVLEN
FPAKPLLEYALEVEKITTSKKPNLILNVDGVIATCFVDMLRNC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4512.t6 CDD cd06100 CCL_ACL-C 159 339 1.58796E-75
7 g4512.t6 Gene3D G3DSA:3.40.50.261 - 1 123 3.5E-39
8 g4512.t6 Gene3D G3DSA:1.10.230.10 - 240 339 5.8E-13
3 g4512.t6 PANTHER PTHR23118:SF0 ATP-CITRATE SYNTHASE 1 343 2.7E-202
4 g4512.t6 PANTHER PTHR23118 ATP-CITRATE SYNTHASE 1 343 2.7E-202
2 g4512.t6 Pfam PF00549 CoA-ligase 2 87 1.3E-8
1 g4512.t6 Pfam PF00285 Citrate synthase, C-terminal domain 188 333 3.9E-18
6 g4512.t6 ProSitePatterns PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site. 49 65 -
5 g4512.t6 SUPERFAMILY SSF48256 Citrate synthase 5 341 6.54E-57

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
GO:0003824 catalytic activity 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.

Raw TPM values