General information for g4512.t15
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.t15 | isoform | g4512.t15 | 2952512 | 2956816 |
| chr_2 | g4512 | g4512.t15 | exon | g4512.t15.exon1 | 2952512 | 2952891 |
| chr_2 | g4512 | g4512.t15 | cds | g4512.t15.CDS1 | 2952513 | 2952891 |
| chr_2 | g4512 | g4512.t15 | exon | g4512.t15.exon2 | 2952957 | 2953333 |
| chr_2 | g4512 | g4512.t15 | cds | g4512.t15.CDS2 | 2952957 | 2953333 |
| chr_2 | g4512 | g4512.t15 | exon | g4512.t15.exon3 | 2954659 | 2954891 |
| chr_2 | g4512 | g4512.t15 | cds | g4512.t15.CDS3 | 2954659 | 2954820 |
| chr_2 | g4512 | g4512.t15 | exon | g4512.t15.exon4 | 2956628 | 2956816 |
| chr_2 | g4512 | g4512.t15 | TSS | g4512.t15 | 2956820 | 2956820 |
| chr_2 | g4512 | g4512.t15 | TTS | g4512.t15 | NA | NA |
Sequences
>g4512.t15 Gene=g4512 Length=1179
AAAAGAGTGAGAGAGGAAGCAAAAGGAAGTGTGTTTCTAGATTTCTAATCACTTATATAG
TATTTAAAAGGGATTCGAAGCTTTTAAAATTATACTTAAGCATCCATCAATTAGTTTAAA
CTATTCTCACTTCAGTATAAAGTGTTTTAAATCATTACACTCAATTAATTGTTCAAAATA
ATTGTATAAATTCGTAAACATCTTTTTGGATGCTGTAACAGCTTAAAATTAGTAATATTG
GTGTGTGATTAAGTGAAATCATGTCAGCTAAAGCGATTCGTGAGGTAACAGGAAAGGAAC
TTATAAACAAATATTTGGGTGGTGTGAACGAAACTGGTGTTCAAAAAAGTCGTTTTGCTG
CTGTCACCGAGAATACAGATTGGAGTCAATTGGTTGCTGAGAATCCATGGCTTGAAAGCA
CACCTCTCGTTGTTAAGCCAGATCAACTTATTAAGCGTCGTGGGAAATTAGGATTGATTG
CAGTCAATAAGAATTTTTCTCAAGTCAAGCAATGGATAAACGAGCGAATGGGAAAAGATC
AAAAAGTTGGAAGTGCAGTTGGCAAACTCCGAAATTTCATTATTGAGCCATTTATACCTC
ACAAGGATGATGAGGAAGCATACGTTTGCATTTATTCACATCGAACGGCAGATACAATCT
TATTTTATCATCAAGGTGGTGTTGACATTGGTGACGTCGATTCAAAGGCTCTTAAGCTCG
ATGTTCCTGTTGGAGCAACAGTCACAGTCGATGATATTCAAAAAACCTTGTTAAAAGAAG
TTGCAACAGCCAAAAAAGCACGTATTGGCAAATTTATTTATGAGCTTTATCAGTTATATT
CTGATCTCTACTTTACATATCTTGAAATTAACCCTCTCGTTGTCACTGATGACTCAATCT
ATATTTTGGATCTTGCTGCCAAAATTGATGCCACTGCTGATTTTATTTGTCGTCCAAAAT
GGGGAGATATTGATTATCCGCCACCCTTTGGACGTGATGCTTATCCCGAAGAAGCATATA
TTGCAGATTTGGATGCCAAATCTGGTGCATCTTTAAAATTAACGATTTTAAATCGTAATG
GTCGTATTTGGACTATGGTTGCTGGTGGTGGTGCAAGTGTTATTTATTCAGATACTATTT
GTGACTATGGTGGAGCTTCAGAATTGGCAAATTATGGCG
>g4512.t15 Gene=g4512 Length=306
MSAKAIREVTGKELINKYLGGVNETGVQKSRFAAVTENTDWSQLVAENPWLESTPLVVKP
DQLIKRRGKLGLIAVNKNFSQVKQWINERMGKDQKVGSAVGKLRNFIIEPFIPHKDDEEA
YVCIYSHRTADTILFYHQGGVDIGDVDSKALKLDVPVGATVTVDDIQKTLLKEVATAKKA
RIGKFIYELYQLYSDLYFTYLEINPLVVTDDSIYILDLAAKIDATADFICRPKWGDIDYP
PPFGRDAYPEEAYIADLDAKSGASLKLTILNRNGRIWTMVAGGGASVIYSDTICDYGGAS
ELANYG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4512.t15 | Gene3D | G3DSA:3.30.470.20 | - | 5 | 243 | 1.4E-101 |
| 9 | g4512.t15 | Gene3D | G3DSA:3.30.1490.20 | - | 32 | 111 | 1.4E-101 |
| 10 | g4512.t15 | Gene3D | G3DSA:3.40.50.261 | - | 247 | 306 | 9.1E-27 |
| 3 | g4512.t15 | PANTHER | PTHR23118 | ATP-CITRATE SYNTHASE | 1 | 306 | 4.6E-132 |
| 4 | g4512.t15 | PANTHER | PTHR23118:SF32 | ATP-CITRATE SYNTHASE | 1 | 306 | 4.6E-132 |
| 2 | g4512.t15 | Pfam | PF08442 | ATP-grasp domain | 24 | 208 | 1.9E-9 |
| 1 | g4512.t15 | Pfam | PF16114 | ATP citrate lyase citrate-binding | 245 | 306 | 2.8E-30 |
| 7 | g4512.t15 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 274 | 299 | - |
| 11 | g4512.t15 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 19 | 233 | 9.136 |
| 5 | g4512.t15 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 5 | 241 | 4.24E-39 |
| 6 | g4512.t15 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 263 | 305 | 3.52E-6 |
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 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.
