General information for g4512.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-citrate synthase.
Parent gene
- The parent gene g4512 is located on chr_2: 2954643..2956816 (- strand)
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.t1 | TTS | g4512.t1 | 2949079 | 2949079 |
| chr_2 | g4512 | g4512.t1 | isoform | g4512.t1 | 2949442 | 2954820 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon1 | 2949442 | 2949619 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS1 | 2949442 | 2949619 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon2 | 2949679 | 2950019 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS2 | 2949679 | 2950019 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon3 | 2950076 | 2950818 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS3 | 2950076 | 2950818 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon4 | 2950890 | 2950972 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS4 | 2950890 | 2950972 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon5 | 2951074 | 2951674 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS5 | 2951074 | 2951674 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon6 | 2951981 | 2952295 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS6 | 2951981 | 2952295 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon7 | 2952359 | 2952891 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS7 | 2952359 | 2952891 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon8 | 2952957 | 2953333 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS8 | 2952957 | 2953333 |
| chr_2 | g4512 | g4512.t1 | exon | g4512.t1.exon9 | 2954659 | 2954820 |
| chr_2 | g4512 | g4512.t1 | cds | g4512.t1.CDS9 | 2954659 | 2954820 |
| chr_2 | g4512 | g4512.t1 | TSS | g4512.t1 | NA | NA |
Sequences
>g4512.t1 Gene=g4512 Length=3333
ATGTCAGCTAAAGCGATTCGTGAGGTAACAGGAAAGGAACTTATAAACAAATATTTGGGT
GGTGTGAACGAAACTGGTGTTCAAAAAAGTCGTTTTGCTGCTGTCACCGAGAATACAGAT
TGGAGTCAATTGGTTGCTGAGAATCCATGGCTTGAAAGCACACCTCTCGTTGTTAAGCCA
GATCAACTTATTAAGCGTCGTGGGAAATTAGGATTGATTGCAGTCAATAAGAATTTTTCT
CAAGTCAAGCAATGGATAAACGAGCGAATGGGAAAAGATCAAAAAGTTGGAAGTGCAGTT
GGCAAACTCCGAAATTTCATTATTGAGCCATTTATACCTCACAAGGATGATGAGGAAGCA
TACGTTTGCATTTATTCACATCGAACGGCAGATACAATCTTATTTTATCATCAAGGTGGT
GTTGACATTGGTGACGTCGATTCAAAGGCTCTTAAGCTCGATGTTCCTGTTGGAGCAACA
GTCACAGTCGATGATATTCAAAAAACCTTGTTAAAAGAAGTTGCAACAGCCAAAAAAGCA
CGTATTGGCAAATTTATTTATGAGCTTTATCAGTTATATTCTGATCTCTACTTTACATAT
CTTGAAATTAACCCTCTCGTTGTCACTGATGACTCAATCTATATTTTGGATCTTGCTGCC
AAAATTGATGCCACTGCTGATTTTATTTGTCGTCCAAAATGGGGAGATATTGATTATCCG
CCACCCTTTGGACGTGATGCTTATCCCGAAGAAGCATATATTGCAGATTTGGATGCCAAA
TCTGGTGCATCTTTAAAATTAACGATTTTAAATCGTAATGGTCGTATTTGGACTATGGTT
GCTGGTGGTGGTGCAAGTGTTATTTATTCAGATACTATTTGTGACTATGGTGGAGCTTCA
GAATTGGCAAATTATGGCGAGTATAGTGGTGCACCTTCAGAACAACAAACTTACGAATAT
GCTAAAACTATTCTCAATCTTATGACATCATCACCTAAACATCCTGATGGAAAAGTTTTG
ATTATTGGAGGTGGAATTGCAAATTTTACAAATGTTGCTGCAACATTCAGTGGAATCATT
ACTGCATTAAGAGAATTTATGGCTCGTTTGATTGAACATAAAGTCTCAGTTTTCGTTCGT
CGTGCTGGTCCAAATTATCAAGAAGGTCTTCGTCGAATGCGTGAAATTGGTGCCACTCTT
GGAATTCCTTTACACGTTTTCGGTCCAGAAACTCATATGACAGCAATTTGTGGAATGGCT
CTTGGCAAAAAACCAATTCCTAATGTTGCTGATTTACACTTTGCAACAGCAAATTTCTTA
TTACCTGGTGGTCAACAACAGCAAGAACAACGTAAAATGATTTCTAGTCAAACATCTCAA
ACTGATGGCACAAAAAGAATTTCATTAAACTCTTCTATAGGTGCATCAGGACAGACATCT
TCTGCAAAAGCCACTCGTGCTGGAGTAACAAATCAGGCTGAATACAGAAAGCTTTTCTCA
AAAAATACAAAATCAATTGTATGGGGAATGCAAACTCGTGCCGTTCAGTCAATGTTAGAT
TTTGATTTTATTTGTCGTCGTGAAGAGCCATCAGTTGTCGCGATGGTTTATCCTTTTACC
GGATATCACCGTCAAAAGTTTTACTGGGGACATAAAGAAATTTTAATTCCCGTCTATAGC
AAAATGGGAGATGCTTGCAGTAAACATAAGGATGTTGATGTTCTTGTTAATTTTGCATCA
CTTAGATCTGCTTATGAATCATCACTCGAGGTTGTCAATGAATTTCCTCAAATTCGTACT
ATTGCAATTATTGCTGAAGGTATACCTGAAAACATGACAAGAAAACTTAATGCAGCCGCT
CATTCCAAAAAGGTCTCTATTATTGGACCTGCCACGGTTGGTGGCGTAAAACCAGGTTGT
TTCAAAATTGGAAATACTGGAGGAATGCTGGATAATATTTTGCATTCAAAATTATACCGT
CCTGGCAGTGTGGCATATGTTTCTCGATCAGGTGGAATGTCAAATGAATTGAACAATATT
ATAAGCAATACAACAGACGGTGTATTTGAAGGTGTTGCAATTGGTGGTGATCGTTATCCC
GGAACAACTTTTATGGATCATATCATGCGTTATCAAAATGATGATGGTGCAAAATTGATT
GTTGTTCTTGGTGAAGTTGGTGGAGTTGAGGAATATGAAATTTGTGCGGCTTTAAAAGAT
GGAAGAATTACAAAGCCATTGATTGCATGGTGCATTGGAACATGTGCTGGAATGTTTACA
TCTGAAGTTCAATTCGGTCATGCTGGTTCATGCGCTCAATCAGATATGGAAACAGCTTCA
GCTAAAAATAAGGCATTACGTGATGCAGGAGCACATGTACCTGATTCTTTTGATACTCTT
GGAGATTTAATTGCTCACGTTTATGAGGATATGGTACAAAGTGGACAAATTGTTCCCGCC
GAAGAAGTTCCACCACCGACCGTTCCTATGGATTATAATTGGGCACGCGAGTTGGGATTG
ATTCGTAAGCCAGCCTCATTCATGACATCGATTTGTGATGAACGTGGACAAGAATTGTTG
TATGCTGGAATGCCAATCAGTGAAGTTTTGACAAAAGATGTCGGTATTGGCGGTGTTGTT
TCACTCTTATGGTTCCAACGTTGTTTACCACCATACGTTTGCAAATTCTTTGAGATGTGT
TTAATGGTAACTGCAGATCACGGACCAGCCGTCAGTGGAGCACACAATACAATTGTCTGT
GCTCGTGCTGGAAAAGACCTTGTATCATCACTCGTGTCAGGATTGTTGACTATTGGTGAC
CGTTTTGGTGGGGCTCTTGATGGCGCAGCAAAACAATTTTCTGAAGCATATGATTCGAAT
ATGCATCCAATGGACTTTGTCAACTCAATGCGTAAAAAGGGTCAACTTATCATGGGTATA
GGTCATCGTGTAAAATCAATCAACAATCCTGATATTCGTGTTAAAATTATCAAAGAGTTT
GTGCTCGAAAACTTCCCAGCTAAGCCACTTTTGGAATATGCATTGGAAGTTGAAAAGATT
ACTACAAGTAAAAAGCCAAACTTGATTTTGAATGTCGACGGTGTCATTGCAACATGCTTC
GTCGATATGTTGAGAAATTGTGGTGCATTCTCAAGTGAAGAGGCACAAGAATATATCAAT
ATTGGTGCTATAAATTCACTCTTTGTGTTGGGTCGTAGTATTGGTTTTATTGGACATTAT
ATGGATCAGAGACGCTTGAAACAAGGACTTTATAGACATCCTTGGGATGACATTTCTTAT
GTTCTTCCTGAACAATATAACTGCAACAATTAA
>g4512.t1 Gene=g4512 Length=1110
MSAKAIREVTGKELINKYLGGVNETGVQKSRFAAVTENTDWSQLVAENPWLESTPLVVKP
DQLIKRRGKLGLIAVNKNFSQVKQWINERMGKDQKVGSAVGKLRNFIIEPFIPHKDDEEA
YVCIYSHRTADTILFYHQGGVDIGDVDSKALKLDVPVGATVTVDDIQKTLLKEVATAKKA
RIGKFIYELYQLYSDLYFTYLEINPLVVTDDSIYILDLAAKIDATADFICRPKWGDIDYP
PPFGRDAYPEEAYIADLDAKSGASLKLTILNRNGRIWTMVAGGGASVIYSDTICDYGGAS
ELANYGEYSGAPSEQQTYEYAKTILNLMTSSPKHPDGKVLIIGGGIANFTNVAATFSGII
TALREFMARLIEHKVSVFVRRAGPNYQEGLRRMREIGATLGIPLHVFGPETHMTAICGMA
LGKKPIPNVADLHFATANFLLPGGQQQQEQRKMISSQTSQTDGTKRISLNSSIGASGQTS
SAKATRAGVTNQAEYRKLFSKNTKSIVWGMQTRAVQSMLDFDFICRREEPSVVAMVYPFT
GYHRQKFYWGHKEILIPVYSKMGDACSKHKDVDVLVNFASLRSAYESSLEVVNEFPQIRT
IAIIAEGIPENMTRKLNAAAHSKKVSIIGPATVGGVKPGCFKIGNTGGMLDNILHSKLYR
PGSVAYVSRSGGMSNELNNIISNTTDGVFEGVAIGGDRYPGTTFMDHIMRYQNDDGAKLI
VVLGEVGGVEEYEICAALKDGRITKPLIAWCIGTCAGMFTSEVQFGHAGSCAQSDMETAS
AKNKALRDAGAHVPDSFDTLGDLIAHVYEDMVQSGQIVPAEEVPPPTVPMDYNWARELGL
IRKPASFMTSICDERGQELLYAGMPISEVLTKDVGIGGVVSLLWFQRCLPPYVCKFFEMC
LMVTADHGPAVSGAHNTIVCARAGKDLVSSLVSGLLTIGDRFGGALDGAAKQFSEAYDSN
MHPMDFVNSMRKKGQLIMGIGHRVKSINNPDIRVKIIKEFVLENFPAKPLLEYALEVEKI
TTSKKPNLILNVDGVIATCFVDMLRNCGAFSSEEAQEYINIGAINSLFVLGRSIGFIGHY
MDQRRLKQGLYRHPWDDISYVLPEQYNCNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g4512.t1 | CDD | cd06100 | CCL_ACL-C | 863 | 1100 | 7.88116E-91 |
| 13 | g4512.t1 | Gene3D | G3DSA:3.30.470.20 | - | 5 | 243 | 2.8E-100 |
| 14 | g4512.t1 | Gene3D | G3DSA:3.30.1490.20 | - | 32 | 111 | 2.8E-100 |
| 16 | g4512.t1 | Gene3D | G3DSA:3.40.50.261 | - | 247 | 409 | 3.8E-78 |
| 12 | g4512.t1 | Gene3D | G3DSA:3.40.50.720 | - | 494 | 631 | 4.4E-61 |
| 15 | g4512.t1 | Gene3D | G3DSA:3.40.50.261 | - | 632 | 827 | 6.2E-70 |
| 17 | g4512.t1 | Gene3D | G3DSA:1.10.230.10 | - | 944 | 1043 | 3.5E-12 |
| 6 | g4512.t1 | PANTHER | PTHR23118:SF16 | ATP-CITRATE SYNTHASE | 1 | 1106 | 0.0 |
| 7 | g4512.t1 | PANTHER | PTHR23118 | ATP-CITRATE SYNTHASE | 1 | 1106 | 0.0 |
| 18 | g4512.t1 | PIRSF | PIRSF036511 | ATP_citrt_syn | 1 | 1108 | 0.0 |
| 5 | g4512.t1 | Pfam | PF08442 | ATP-grasp domain | 24 | 208 | 2.8E-8 |
| 4 | g4512.t1 | Pfam | PF16114 | ATP citrate lyase citrate-binding | 245 | 423 | 2.3E-90 |
| 3 | g4512.t1 | Pfam | PF02629 | CoA binding domain | 501 | 607 | 3.1E-7 |
| 2 | g4512.t1 | Pfam | PF00549 | CoA-ligase | 667 | 791 | 6.4E-15 |
| 1 | g4512.t1 | Pfam | PF00285 | Citrate synthase, C-terminal domain | 892 | 1090 | 1.7E-19 |
| 20 | g4512.t1 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 274 | 299 | - |
| 22 | g4512.t1 | ProSitePatterns | PS01216 | ATP-citrate lyase / succinyl-CoA ligases family signature 1. | 668 | 697 | - |
| 21 | g4512.t1 | ProSitePatterns | PS00399 | ATP-citrate lyase / succinyl-CoA ligases family active site. | 753 | 769 | - |
| 23 | g4512.t1 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 19 | 233 | 9.136 |
| 10 | g4512.t1 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 5 | 241 | 1.71E-37 |
| 11 | g4512.t1 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 263 | 399 | 1.16E-22 |
| 9 | g4512.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 498 | 630 | 9.06E-17 |
| 8 | g4512.t1 | SUPERFAMILY | SSF48256 | Citrate synthase | 625 | 1102 | 2.49E-80 |
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:0006101 | citrate metabolic process | BP |
| GO:0006085 | acetyl-CoA biosynthetic process | BP |
| GO:0003878 | ATP citrate synthase activity | MF |
| GO:0046872 | metal ion binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0046912 | acyltransferase, acyl groups converted into alkyl on transfer | MF |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01648 (ATP citrate (pro-S)-lyase)
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.
