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.t4 isoform g4512.t4 2949028 2950363
chr_2 g4512 g4512.t4 exon g4512.t4.exon1 2949028 2949619
chr_2 g4512 g4512.t4 cds g4512.t4.CDS1 2949442 2949619
chr_2 g4512 g4512.t4 exon g4512.t4.exon2 2949679 2950019
chr_2 g4512 g4512.t4 cds g4512.t4.CDS2 2949679 2950019
chr_2 g4512 g4512.t4 exon g4512.t4.exon3 2950076 2950363
chr_2 g4512 g4512.t4 cds g4512.t4.CDS3 2950076 2950348
chr_2 g4512 g4512.t4 TSS g4512.t4 NA NA
chr_2 g4512 g4512.t4 TTS g4512.t4 NA NA

Sequences

>g4512.t4 Gene=g4512 Length=1221
AAGCCAGCCTCATTCATGACATCGATTTGTGATGAACGTGGACAAGAATTGTTGTATGCT
GGAATGCCAATCAGTGAAGTTTTGACAAAAGATGTCGGTATTGGCGGTGTTGTTTCACTC
TTATGGTTCCAACGTTGTTTACCACCATACGTTTGCAAATTCTTTGAGATGTGTTTAATG
GTAACTGCAGATCACGGACCAGCCGTCAGTGGAGCACACAATACAATTGTCTGTGCTCGT
GCTGGAAAAGACCTTGTATCATCACTCGTGTCAGGATTGTTGACTATTGGTGACCGTTTT
GGTGGGGCTCTTGATGGCGCAGCAAAACAATTTTCTGAAGCATATGATTCGAATATGCAT
CCAATGGACTTTGTCAACTCAATGCGTAAAAAGGGTCAACTTATCATGGGTATAGGTCAT
CGTGTAAAATCAATCAACAATCCTGATATTCGTGTTAAAATTATCAAAGAGTTTGTGCTC
GAAAACTTCCCAGCTAAGCCACTTTTGGAATATGCATTGGAAGTTGAAAAGATTACTACA
AGTAAAAAGCCAAACTTGATTTTGAATGTCGACGGTGTCATTGCAACATGCTTCGTCGAT
ATGTTGAGAAATTGTGGTGCATTCTCAAGTGAAGAGGCACAAGAATATATCAATATTGGT
GCTATAAATTCACTCTTTGTGTTGGGTCGTAGTATTGGTTTTATTGGACATTATATGGAT
CAGAGACGCTTGAAACAAGGACTTTATAGACATCCTTGGGATGACATTTCTTATGTTCTT
CCTGAACAATATAACTGCAACAATTAAACACTCTATCTATTATACTTGATCATAAAGATT
TTTTTTTCTCAATATTTTATAATTTTATCTCAGCATTTCTCTCGTACATGCACTTTTTTT
ATTTTACATTTTATGGATAAATTATGGGTTTAGGTAGATTATTGTGTCTTTAAAAGATGT
TATGTTGATTTTTATTATTTCAAAAATCGATAACTGAAAGAAAAGATTATTAACATTTTA
ACTAAACATGATAAAAAGTACTATGAATTAAAGGATCAAGAAAAAATCTAAATGTTATGT
AGGATAAAAATTGCTTTTGCACAAATATTTGTAGAAGTTTTTTTGCACAAGAAAGAAAAG
AATATAACATTCCTTTAGAGGAAAAATGAAAGAAAAAAAAATGATATATATATATATATA
TATTATACATAATTATTTTTT

>g4512.t4 Gene=g4512 Length=263
MTSICDERGQELLYAGMPISEVLTKDVGIGGVVSLLWFQRCLPPYVCKFFEMCLMVTADH
GPAVSGAHNTIVCARAGKDLVSSLVSGLLTIGDRFGGALDGAAKQFSEAYDSNMHPMDFV
NSMRKKGQLIMGIGHRVKSINNPDIRVKIIKEFVLENFPAKPLLEYALEVEKITTSKKPN
LILNVDGVIATCFVDMLRNCGAFSSEEAQEYINIGAINSLFVLGRSIGFIGHYMDQRRLK
QGLYRHPWDDISYVLPEQYNCNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g4512.t4 CDD cd06100 CCL_ACL-C 16 253 0
5 g4512.t4 Gene3D G3DSA:1.10.230.10 - 97 196 0
2 g4512.t4 PANTHER PTHR23118:SF0 ATP-CITRATE SYNTHASE 1 258 0
3 g4512.t4 PANTHER PTHR23118 ATP-CITRATE SYNTHASE 1 258 0
1 g4512.t4 Pfam PF00285 Citrate synthase, C-terminal domain 45 244 0
4 g4512.t4 SUPERFAMILY SSF48256 Citrate synthase 3 255 0

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.

Raw TPM values