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.t7 TTS g4512.t7 2949079 2949079
chr_2 g4512 g4512.t7 isoform g4512.t7 2950081 2952512
chr_2 g4512 g4512.t7 exon g4512.t7.exon1 2950081 2950818
chr_2 g4512 g4512.t7 cds g4512.t7.CDS1 2950082 2950818
chr_2 g4512 g4512.t7 exon g4512.t7.exon2 2950890 2950972
chr_2 g4512 g4512.t7 cds g4512.t7.CDS2 2950890 2950972
chr_2 g4512 g4512.t7 exon g4512.t7.exon3 2951074 2951674
chr_2 g4512 g4512.t7 cds g4512.t7.CDS3 2951074 2951674
chr_2 g4512 g4512.t7 exon g4512.t7.exon4 2951981 2952295
chr_2 g4512 g4512.t7 cds g4512.t7.CDS4 2951981 2952295
chr_2 g4512 g4512.t7 exon g4512.t7.exon5 2952359 2952512
chr_2 g4512 g4512.t7 cds g4512.t7.CDS5 2952359 2952449
chr_2 g4512 g4512.t7 TSS g4512.t7 NA NA

Sequences

>g4512.t7 Gene=g4512 Length=1891
GAGTATAGTGGTGCACCTTCAGAACAACAAACTTACGAATATGCTAAAACTATTCTCAAT
CTTATGACATCATCACCTAAACATCCTGATGGAAAAGTTTTGATTATTGGAGGTGGAATT
GCAAATTTTACAAATGTTGCTGCAACATTCAGTGGAATCATTACTGCATTAAGAGAATTT
ATGGCTCGTTTGATTGAACATAAAGTCTCAGTTTTCGTTCGTCGTGCTGGTCCAAATTAT
CAAGAAGGTCTTCGTCGAATGCGTGAAATTGGTGCCACTCTTGGAATTCCTTTACACGTT
TTCGGTCCAGAAACTCATATGACAGCAATTTGTGGAATGGCTCTTGGCAAAAAACCAATT
CCTAATGTTGCTGATTTACACTTTGCAACAGCAAATTTCTTATTACCTGGTGGTCAACAA
CAGCAAGAACAACGTAAAATGATTTCTAGTCAAACATCTCAAACTGATGGCACAAAAAGA
ATTTCATTAAACTCTTCTATAGGTGCATCAGGACAGACATCTTCTGCAAAAGCCACTCGT
GCTGGAGTAACAAATCAGGCTGAATACAGAAAGCTTTTCTCAAAAAATACAAAATCAATT
GTATGGGGAATGCAAACTCGTGCCGTTCAGTCAATGTTAGATTTTGATTTTATTTGTCGT
CGTGAAGAGCCATCAGTTGTCGCGATGGTTTATCCTTTTACCGGATATCACCGTCAAAAG
TTTTACTGGGGACATAAAGAAATTTTAATTCCCGTCTATAGCAAAATGGGAGATGCTTGC
AGTAAACATAAGGATGTTGATGTTCTTGTTAATTTTGCATCACTTAGATCTGCTTATGAA
TCATCACTCGAGGTTGTCAATGAATTTCCTCAAATTCGTACTATTGCAATTATTGCTGAA
GGTATACCTGAAAACATGACAAGAAAACTTAATGCAGCCGCTCATTCCAAAAAGGTCTCT
ATTATTGGACCTGCCACGGTTGGTGGCGTAAAACCAGGTTGTTTCAAAATTGGAAATACT
GGAGGAATGCTGGATAATATTTTGCATTCAAAATTATACCGTCCTGGCAGTGTGGCATAT
GTTTCTCGATCAGGTGGAATGTCAAATGAATTGAACAATATTATAAGCAATACAACAGAC
GGTGTATTTGAAGGTGTTGCAATTGGTGGTGATCGTTATCCCGGAACAACTTTTATGGAT
CATATCATGCGTTATCAAAATGATGATGGTGCAAAATTGATTGTTGTTCTTGGTGAAGTT
GGTGGAGTTGAGGAATATGAAATTTGTGCGGCTTTAAAAGATGGAAGAATTACAAAGCCA
TTGATTGCATGGTGCATTGGAACATGTGCTGGAATGTTTACATCTGAAGTTCAATTCGGT
CATGCTGGTTCATGCGCTCAATCAGATATGGAAACAGCTTCAGCTAAAAATAAGGCATTA
CGTGATGCAGGAGCACATGTACCTGATTCTTTTGATACTCTTGGAGATTTAATTGCTCAC
GTTTATGAGGATATGGTACAAAGTGGACAAATTGTTCCCGCCGAAGAAGTTCCACCACCG
ACCGTTCCTATGGATTATAATTGGGCACGCGAGTTGGGATTGATTCGTAAGCCAGCCTCA
TTCATGACATCGATTTGTGATGAACGTGGACAAGAATTGTTGTATGCTGGAATGCCAATC
AGTGAAGTTTTGACAAAAGATGTCGGTATTGGCGGTGTTGTTTCACTCTTATGGTTCCAA
CGTTGTTTACCACCATACGTTTGCAAATTCTTTGAGATGTGTTTAATGGTAACTGCAGAT
CACGGACCAGCCGTCAGTGGAGCACACAATACAATTGTCTGTGCTCGTGCTGGAAAAGAC
CTTGTATCATCACTCGTGTCAGGATTGTTGA

>g4512.t7 Gene=g4512 Length=609
MTSSPKHPDGKVLIIGGGIANFTNVAATFSGIITALREFMARLIEHKVSVFVRRAGPNYQ
EGLRRMREIGATLGIPLHVFGPETHMTAICGMALGKKPIPNVADLHFATANFLLPGGQQQ
QEQRKMISSQTSQTDGTKRISLNSSIGASGQTSSAKATRAGVTNQAEYRKLFSKNTKSIV
WGMQTRAVQSMLDFDFICRREEPSVVAMVYPFTGYHRQKFYWGHKEILIPVYSKMGDACS
KHKDVDVLVNFASLRSAYESSLEVVNEFPQIRTIAIIAEGIPENMTRKLNAAAHSKKVSI
IGPATVGGVKPGCFKIGNTGGMLDNILHSKLYRPGSVAYVSRSGGMSNELNNIISNTTDG
VFEGVAIGGDRYPGTTFMDHIMRYQNDDGAKLIVVLGEVGGVEEYEICAALKDGRITKPL
IAWCIGTCAGMFTSEVQFGHAGSCAQSDMETASAKNKALRDAGAHVPDSFDTLGDLIAHV
YEDMVQSGQIVPAEEVPPPTVPMDYNWARELGLIRKPASFMTSICDERGQELLYAGMPIS
EVLTKDVGIGGVVSLLWFQRCLPPYVCKFFEMCLMVTADHGPAVSGAHNTIVCARAGKDL
VSSLVSGLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g4512.t7 Gene3D G3DSA:3.40.50.261 - 1 82 3.2E-30
12 g4512.t7 Gene3D G3DSA:3.40.50.720 - 167 304 1.7E-61
13 g4512.t7 Gene3D G3DSA:3.40.50.261 - 305 500 2.2E-70
4 g4512.t7 PANTHER PTHR23118:SF16 ATP-CITRATE SYNTHASE 5 609 0.0
5 g4512.t7 PANTHER PTHR23118 ATP-CITRATE SYNTHASE 5 609 0.0
3 g4512.t7 Pfam PF16114 ATP citrate lyase citrate-binding 3 96 4.7E-39
2 g4512.t7 Pfam PF02629 CoA binding domain 174 280 1.3E-7
1 g4512.t7 Pfam PF00549 CoA-ligase 340 464 2.6E-15
16 g4512.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
17 g4512.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 36 -
15 g4512.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 37 609 -
11 g4512.t7 ProSitePatterns PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1. 341 370 -
10 g4512.t7 ProSitePatterns PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site. 426 442 -
9 g4512.t7 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 5 72 2.9E-7
8 g4512.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 171 303 3.54E-17
7 g4512.t7 SUPERFAMILY SSF48256 Citrate synthase 298 608 9.73E-36
6 g4512.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -

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