General information for g4512.t12
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.t12 | isoform | g4512.t12 | 2951979 | 2954820 |
| chr_2 | g4512 | g4512.t12 | exon | g4512.t12.exon1 | 2951979 | 2952295 |
| chr_2 | g4512 | g4512.t12 | cds | g4512.t12.CDS1 | 2951979 | 2952295 |
| chr_2 | g4512 | g4512.t12 | exon | g4512.t12.exon2 | 2952359 | 2952891 |
| chr_2 | g4512 | g4512.t12 | cds | g4512.t12.CDS2 | 2952359 | 2952891 |
| chr_2 | g4512 | g4512.t12 | exon | g4512.t12.exon3 | 2952957 | 2953333 |
| chr_2 | g4512 | g4512.t12 | cds | g4512.t12.CDS3 | 2952957 | 2953333 |
| chr_2 | g4512 | g4512.t12 | exon | g4512.t12.exon4 | 2954659 | 2954820 |
| chr_2 | g4512 | g4512.t12 | cds | g4512.t12.CDS4 | 2954659 | 2954820 |
| chr_2 | g4512 | g4512.t12 | TSS | g4512.t12 | NA | NA |
| chr_2 | g4512 | g4512.t12 | TTS | g4512.t12 | NA | NA |
Sequences
>g4512.t12 Gene=g4512 Length=1389
ATGTCAGCTAAAGCGATTCGTGAGGTAACAGGAAAGGAACTTATAAACAAATATTTGGGT
GGTGTGAACGAAACTGGTGTTCAAAAAAGTCGTTTTGCTGCTGTCACCGAGAATACAGAT
TGGAGTCAATTGGTTGCTGAGAATCCATGGCTTGAAAGCACACCTCTCGTTGTTAAGCCA
GATCAACTTATTAAGCGTCGTGGGAAATTAGGATTGATTGCAGTCAATAAGAATTTTTCT
CAAGTCAAGCAATGGATAAACGAGCGAATGGGAAAAGATCAAAAAGTTGGAAGTGCAGTT
GGCAAACTCCGAAATTTCATTATTGAGCCATTTATACCTCACAAGGATGATGAGGAAGCA
TACGTTTGCATTTATTCACATCGAACGGCAGATACAATCTTATTTTATCATCAAGGTGGT
GTTGACATTGGTGACGTCGATTCAAAGGCTCTTAAGCTCGATGTTCCTGTTGGAGCAACA
GTCACAGTCGATGATATTCAAAAAACCTTGTTAAAAGAAGTTGCAACAGCCAAAAAAGCA
CGTATTGGCAAATTTATTTATGAGCTTTATCAGTTATATTCTGATCTCTACTTTACATAT
CTTGAAATTAACCCTCTCGTTGTCACTGATGACTCAATCTATATTTTGGATCTTGCTGCC
AAAATTGATGCCACTGCTGATTTTATTTGTCGTCCAAAATGGGGAGATATTGATTATCCG
CCACCCTTTGGACGTGATGCTTATCCCGAAGAAGCATATATTGCAGATTTGGATGCCAAA
TCTGGTGCATCTTTAAAATTAACGATTTTAAATCGTAATGGTCGTATTTGGACTATGGTT
GCTGGTGGTGGTGCAAGTGTTATTTATTCAGATACTATTTGTGACTATGGTGGAGCTTCA
GAATTGGCAAATTATGGCGAGTATAGTGGTGCACCTTCAGAACAACAAACTTACGAATAT
GCTAAAACTATTCTCAATCTTATGACATCATCACCTAAACATCCTGATGGAAAAGTTTTG
ATTATTGGAGGTGGAATTGCAAATTTTACAAATGTTGCTGCAACATTCAGTGGAATCATT
ACTGCATTAAGAGAATTTATGGCTCGTTTGATTGAACATAAAGTCTCAGTTTTCGTTCGT
CGTGCTGGTCCAAATTATCAAGAAGGTCTTCGTCGAATGCGTGAAATTGGTGCCACTCTT
GGAATTCCTTTACACGTTTTCGGTCCAGAAACTCATATGACAGCAATTTGTGGAATGGCT
CTTGGCAAAAAACCAATTCCTAATGTTGCTGATTTACACTTTGCAACAGCAAATTTCTTA
TTACCTGGTGGTCAACAACAGCAAGAACAACGTAAAATGATTTCTAGTCAAACATCTCAA
ACTGATGGT
>g4512.t12 Gene=g4512 Length=463
MSAKAIREVTGKELINKYLGGVNETGVQKSRFAAVTENTDWSQLVAENPWLESTPLVVKP
DQLIKRRGKLGLIAVNKNFSQVKQWINERMGKDQKVGSAVGKLRNFIIEPFIPHKDDEEA
YVCIYSHRTADTILFYHQGGVDIGDVDSKALKLDVPVGATVTVDDIQKTLLKEVATAKKA
RIGKFIYELYQLYSDLYFTYLEINPLVVTDDSIYILDLAAKIDATADFICRPKWGDIDYP
PPFGRDAYPEEAYIADLDAKSGASLKLTILNRNGRIWTMVAGGGASVIYSDTICDYGGAS
ELANYGEYSGAPSEQQTYEYAKTILNLMTSSPKHPDGKVLIIGGGIANFTNVAATFSGII
TALREFMARLIEHKVSVFVRRAGPNYQEGLRRMREIGATLGIPLHVFGPETHMTAICGMA
LGKKPIPNVADLHFATANFLLPGGQQQQEQRKMISSQTSQTDG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4512.t12 | Gene3D | G3DSA:3.30.470.20 | - | 5 | 243 | 4.7E-101 |
| 10 | g4512.t12 | Gene3D | G3DSA:3.30.1490.20 | - | 32 | 111 | 4.7E-101 |
| 11 | g4512.t12 | Gene3D | G3DSA:3.40.50.261 | - | 247 | 409 | 8.4E-79 |
| 8 | g4512.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 444 | 463 | - |
| 3 | g4512.t12 | PANTHER | PTHR23118 | ATP-CITRATE SYNTHASE | 1 | 444 | 5.4E-200 |
| 4 | g4512.t12 | PANTHER | PTHR23118:SF32 | ATP-CITRATE SYNTHASE | 1 | 444 | 5.4E-200 |
| 2 | g4512.t12 | Pfam | PF08442 | ATP-grasp domain | 24 | 208 | 5.4E-9 |
| 1 | g4512.t12 | Pfam | PF16114 | ATP citrate lyase citrate-binding | 245 | 423 | 4.8E-91 |
| 7 | g4512.t12 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 274 | 299 | - |
| 12 | g4512.t12 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 19 | 233 | 9.136 |
| 5 | g4512.t12 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 5 | 241 | 1.88E-38 |
| 6 | g4512.t12 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 263 | 399 | 6.1E-23 |
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 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.
