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.t9 isoform g4512.t9 2951081 2956816
chr_2 g4512 g4512.t9 exon g4512.t9.exon1 2951081 2951674
chr_2 g4512 g4512.t9 cds g4512.t9.CDS1 2951082 2951674
chr_2 g4512 g4512.t9 exon g4512.t9.exon2 2951981 2952295
chr_2 g4512 g4512.t9 cds g4512.t9.CDS2 2951981 2952295
chr_2 g4512 g4512.t9 exon g4512.t9.exon3 2952359 2952891
chr_2 g4512 g4512.t9 cds g4512.t9.CDS3 2952359 2952891
chr_2 g4512 g4512.t9 exon g4512.t9.exon4 2952957 2953333
chr_2 g4512 g4512.t9 cds g4512.t9.CDS4 2952957 2953333
chr_2 g4512 g4512.t9 exon g4512.t9.exon5 2954659 2954891
chr_2 g4512 g4512.t9 cds g4512.t9.CDS5 2954659 2954820
chr_2 g4512 g4512.t9 exon g4512.t9.exon6 2956628 2956816
chr_2 g4512 g4512.t9 TSS g4512.t9 2956820 2956820
chr_2 g4512 g4512.t9 TTS g4512.t9 NA NA

Sequences

>g4512.t9 Gene=g4512 Length=2241
AAAAGAGTGAGAGAGGAAGCAAAAGGAAGTGTGTTTCTAGATTTCTAATCACTTATATAG
TATTTAAAAGGGATTCGAAGCTTTTAAAATTATACTTAAGCATCCATCAATTAGTTTAAA
CTATTCTCACTTCAGTATAAAGTGTTTTAAATCATTACACTCAATTAATTGTTCAAAATA
ATTGTATAAATTCGTAAACATCTTTTTGGATGCTGTAACAGCTTAAAATTAGTAATATTG
GTGTGTGATTAAGTGAAATCATGTCAGCTAAAGCGATTCGTGAGGTAACAGGAAAGGAAC
TTATAAACAAATATTTGGGTGGTGTGAACGAAACTGGTGTTCAAAAAAGTCGTTTTGCTG
CTGTCACCGAGAATACAGATTGGAGTCAATTGGTTGCTGAGAATCCATGGCTTGAAAGCA
CACCTCTCGTTGTTAAGCCAGATCAACTTATTAAGCGTCGTGGGAAATTAGGATTGATTG
CAGTCAATAAGAATTTTTCTCAAGTCAAGCAATGGATAAACGAGCGAATGGGAAAAGATC
AAAAAGTTGGAAGTGCAGTTGGCAAACTCCGAAATTTCATTATTGAGCCATTTATACCTC
ACAAGGATGATGAGGAAGCATACGTTTGCATTTATTCACATCGAACGGCAGATACAATCT
TATTTTATCATCAAGGTGGTGTTGACATTGGTGACGTCGATTCAAAGGCTCTTAAGCTCG
ATGTTCCTGTTGGAGCAACAGTCACAGTCGATGATATTCAAAAAACCTTGTTAAAAGAAG
TTGCAACAGCCAAAAAAGCACGTATTGGCAAATTTATTTATGAGCTTTATCAGTTATATT
CTGATCTCTACTTTACATATCTTGAAATTAACCCTCTCGTTGTCACTGATGACTCAATCT
ATATTTTGGATCTTGCTGCCAAAATTGATGCCACTGCTGATTTTATTTGTCGTCCAAAAT
GGGGAGATATTGATTATCCGCCACCCTTTGGACGTGATGCTTATCCCGAAGAAGCATATA
TTGCAGATTTGGATGCCAAATCTGGTGCATCTTTAAAATTAACGATTTTAAATCGTAATG
GTCGTATTTGGACTATGGTTGCTGGTGGTGGTGCAAGTGTTATTTATTCAGATACTATTT
GTGACTATGGTGGAGCTTCAGAATTGGCAAATTATGGCGAGTATAGTGGTGCACCTTCAG
AACAACAAACTTACGAATATGCTAAAACTATTCTCAATCTTATGACATCATCACCTAAAC
ATCCTGATGGAAAAGTTTTGATTATTGGAGGTGGAATTGCAAATTTTACAAATGTTGCTG
CAACATTCAGTGGAATCATTACTGCATTAAGAGAATTTATGGCTCGTTTGATTGAACATA
AAGTCTCAGTTTTCGTTCGTCGTGCTGGTCCAAATTATCAAGAAGGTCTTCGTCGAATGC
GTGAAATTGGTGCCACTCTTGGAATTCCTTTACACGTTTTCGGTCCAGAAACTCATATGA
CAGCAATTTGTGGAATGGCTCTTGGCAAAAAACCAATTCCTAATGTTGCTGATTTACACT
TTGCAACAGCAAATTTCTTATTACCTGGTGGTCAACAACAGCAAGAACAACGTAAAATGA
TTTCTAGTCAAACATCTCAAACTGATGGCACAAAAAGAATTTCATTAAACTCTTCTATAG
GTGCATCAGGACAGACATCTTCTGCAAAAGCCACTCGTGCTGGAGTAACAAATCAGGCTG
AATACAGAAAGCTTTTCTCAAAAAATACAAAATCAATTGTATGGGGAATGCAAACTCGTG
CCGTTCAGTCAATGTTAGATTTTGATTTTATTTGTCGTCGTGAAGAGCCATCAGTTGTCG
CGATGGTTTATCCTTTTACCGGATATCACCGTCAAAAGTTTTACTGGGGACATAAAGAAA
TTTTAATTCCCGTCTATAGCAAAATGGGAGATGCTTGCAGTAAACATAAGGATGTTGATG
TTCTTGTTAATTTTGCATCACTTAGATCTGCTTATGAATCATCACTCGAGGTTGTCAATG
AATTTCCTCAAATTCGTACTATTGCAATTATTGCTGAAGGTATACCTGAAAACATGACAA
GAAAACTTAATGCAGCCGCTCATTCCAAAAAGGTCTCTATTATTGGACCTGCCACGGTTG
GTGGCGTAAAACCAGGTTGTTTCAAAATTGGAAATACTGGAGGAATGCTGGATAATATTT
TGCATTCAAAATTATACCGTC

>g4512.t9 Gene=g4512 Length=660
MSAKAIREVTGKELINKYLGGVNETGVQKSRFAAVTENTDWSQLVAENPWLESTPLVVKP
DQLIKRRGKLGLIAVNKNFSQVKQWINERMGKDQKVGSAVGKLRNFIIEPFIPHKDDEEA
YVCIYSHRTADTILFYHQGGVDIGDVDSKALKLDVPVGATVTVDDIQKTLLKEVATAKKA
RIGKFIYELYQLYSDLYFTYLEINPLVVTDDSIYILDLAAKIDATADFICRPKWGDIDYP
PPFGRDAYPEEAYIADLDAKSGASLKLTILNRNGRIWTMVAGGGASVIYSDTICDYGGAS
ELANYGEYSGAPSEQQTYEYAKTILNLMTSSPKHPDGKVLIIGGGIANFTNVAATFSGII
TALREFMARLIEHKVSVFVRRAGPNYQEGLRRMREIGATLGIPLHVFGPETHMTAICGMA
LGKKPIPNVADLHFATANFLLPGGQQQQEQRKMISSQTSQTDGTKRISLNSSIGASGQTS
SAKATRAGVTNQAEYRKLFSKNTKSIVWGMQTRAVQSMLDFDFICRREEPSVVAMVYPFT
GYHRQKFYWGHKEILIPVYSKMGDACSKHKDVDVLVNFASLRSAYESSLEVVNEFPQIRT
IAIIAEGIPENMTRKLNAAAHSKKVSIIGPATVGGVKPGCFKIGNTGGMLDNILHSKLYR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4512.t9 Gene3D G3DSA:3.30.470.20 - 5 243 1.1E-100
12 g4512.t9 Gene3D G3DSA:3.30.1490.20 - 32 111 1.1E-100
13 g4512.t9 Gene3D G3DSA:3.40.50.261 - 247 409 1.7E-78
10 g4512.t9 Gene3D G3DSA:3.40.50.720 - 494 631 2.0E-61
4 g4512.t9 PANTHER PTHR23118:SF16 ATP-CITRATE SYNTHASE 1 660 5.3E-290
5 g4512.t9 PANTHER PTHR23118 ATP-CITRATE SYNTHASE 1 660 5.3E-290
3 g4512.t9 Pfam PF08442 ATP-grasp domain 24 208 1.1E-8
2 g4512.t9 Pfam PF16114 ATP citrate lyase citrate-binding 245 423 9.8E-91
1 g4512.t9 Pfam PF02629 CoA binding domain 501 607 1.5E-7
9 g4512.t9 ProSitePatterns PS01217 ATP-citrate lyase / succinyl-CoA ligases family signature 3. 274 299 -
14 g4512.t9 ProSiteProfiles PS50975 ATP-grasp fold profile. 19 233 9.136
7 g4512.t9 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 5 241 4.36E-38
8 g4512.t9 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains 263 399 1.19E-22
6 g4512.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 498 630 4.07E-17

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

Pathway

  • This transcript belongs to the following pathways

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