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.t14 isoform g4512.t14 2952512 2954820
chr_2 g4512 g4512.t14 exon g4512.t14.exon1 2952512 2952891
chr_2 g4512 g4512.t14 cds g4512.t14.CDS1 2952513 2952891
chr_2 g4512 g4512.t14 exon g4512.t14.exon2 2952957 2953333
chr_2 g4512 g4512.t14 cds g4512.t14.CDS2 2952957 2953333
chr_2 g4512 g4512.t14 exon g4512.t14.exon3 2954659 2954820
chr_2 g4512 g4512.t14 cds g4512.t14.CDS3 2954659 2954820
chr_2 g4512 g4512.t14 TSS g4512.t14 NA NA
chr_2 g4512 g4512.t14 TTS g4512.t14 NA NA

Sequences

>g4512.t14 Gene=g4512 Length=919
ATGTCAGCTAAAGCGATTCGTGAGGTAACAGGAAAGGAACTTATAAACAAATATTTGGGT
GGTGTGAACGAAACTGGTGTTCAAAAAAGTCGTTTTGCTGCTGTCACCGAGAATACAGAT
TGGAGTCAATTGGTTGCTGAGAATCCATGGCTTGAAAGCACACCTCTCGTTGTTAAGCCA
GATCAACTTATTAAGCGTCGTGGGAAATTAGGATTGATTGCAGTCAATAAGAATTTTTCT
CAAGTCAAGCAATGGATAAACGAGCGAATGGGAAAAGATCAAAAAGTTGGAAGTGCAGTT
GGCAAACTCCGAAATTTCATTATTGAGCCATTTATACCTCACAAGGATGATGAGGAAGCA
TACGTTTGCATTTATTCACATCGAACGGCAGATACAATCTTATTTTATCATCAAGGTGGT
GTTGACATTGGTGACGTCGATTCAAAGGCTCTTAAGCTCGATGTTCCTGTTGGAGCAACA
GTCACAGTCGATGATATTCAAAAAACCTTGTTAAAAGAAGTTGCAACAGCCAAAAAAGCA
CGTATTGGCAAATTTATTTATGAGCTTTATCAGTTATATTCTGATCTCTACTTTACATAT
CTTGAAATTAACCCTCTCGTTGTCACTGATGACTCAATCTATATTTTGGATCTTGCTGCC
AAAATTGATGCCACTGCTGATTTTATTTGTCGTCCAAAATGGGGAGATATTGATTATCCG
CCACCCTTTGGACGTGATGCTTATCCCGAAGAAGCATATATTGCAGATTTGGATGCCAAA
TCTGGTGCATCTTTAAAATTAACGATTTTAAATCGTAATGGTCGTATTTGGACTATGGTT
GCTGGTGGTGGTGCAAGTGTTATTTATTCAGATACTATTTGTGACTATGGTGGAGCTTCA
GAATTGGCAAATTATGGCG

>g4512.t14 Gene=g4512 Length=306
MSAKAIREVTGKELINKYLGGVNETGVQKSRFAAVTENTDWSQLVAENPWLESTPLVVKP
DQLIKRRGKLGLIAVNKNFSQVKQWINERMGKDQKVGSAVGKLRNFIIEPFIPHKDDEEA
YVCIYSHRTADTILFYHQGGVDIGDVDSKALKLDVPVGATVTVDDIQKTLLKEVATAKKA
RIGKFIYELYQLYSDLYFTYLEINPLVVTDDSIYILDLAAKIDATADFICRPKWGDIDYP
PPFGRDAYPEEAYIADLDAKSGASLKLTILNRNGRIWTMVAGGGASVIYSDTICDYGGAS
ELANYG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4512.t14 Gene3D G3DSA:3.30.470.20 - 5 243 1.4E-101
9 g4512.t14 Gene3D G3DSA:3.30.1490.20 - 32 111 1.4E-101
10 g4512.t14 Gene3D G3DSA:3.40.50.261 - 247 306 9.1E-27
3 g4512.t14 PANTHER PTHR23118 ATP-CITRATE SYNTHASE 1 306 4.6E-132
4 g4512.t14 PANTHER PTHR23118:SF32 ATP-CITRATE SYNTHASE 1 306 4.6E-132
2 g4512.t14 Pfam PF08442 ATP-grasp domain 24 208 1.9E-9
1 g4512.t14 Pfam PF16114 ATP citrate lyase citrate-binding 245 306 2.8E-30
7 g4512.t14 ProSitePatterns PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3. 274 299 -
11 g4512.t14 ProSiteProfiles PS50975 ATP-grasp fold profile. 19 233 9.136
5 g4512.t14 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 5 241 4.24E-39
6 g4512.t14 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 263 305 3.52E-6

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:0046872 metal ion binding MF
GO:0005524 ATP binding 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