General information for g4512.t3
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.t3 | isoform | g4512.t3 | 2949028 | 2950019 |
| chr_2 | g4512 | g4512.t3 | exon | g4512.t3.exon1 | 2949028 | 2949619 |
| chr_2 | g4512 | g4512.t3 | cds | g4512.t3.CDS1 | 2949442 | 2949619 |
| chr_2 | g4512 | g4512.t3 | exon | g4512.t3.exon2 | 2949679 | 2950019 |
| chr_2 | g4512 | g4512.t3 | cds | g4512.t3.CDS2 | 2949679 | 2949953 |
| chr_2 | g4512 | g4512.t3 | TSS | g4512.t3 | NA | NA |
| chr_2 | g4512 | g4512.t3 | TTS | g4512.t3 | NA | NA |
Sequences
>g4512.t3 Gene=g4512 Length=933
GGTGACCGTTTTGGTGGGGCTCTTGATGGCGCAGCAAAACAATTTTCTGAAGCATATGAT
TCGAATATGCATCCAATGGACTTTGTCAACTCAATGCGTAAAAAGGGTCAACTTATCATG
GGTATAGGTCATCGTGTAAAATCAATCAACAATCCTGATATTCGTGTTAAAATTATCAAA
GAGTTTGTGCTCGAAAACTTCCCAGCTAAGCCACTTTTGGAATATGCATTGGAAGTTGAA
AAGATTACTACAAGTAAAAAGCCAAACTTGATTTTGAATGTCGACGGTGTCATTGCAACA
TGCTTCGTCGATATGTTGAGAAATTGTGGTGCATTCTCAAGTGAAGAGGCACAAGAATAT
ATCAATATTGGTGCTATAAATTCACTCTTTGTGTTGGGTCGTAGTATTGGTTTTATTGGA
CATTATATGGATCAGAGACGCTTGAAACAAGGACTTTATAGACATCCTTGGGATGACATT
TCTTATGTTCTTCCTGAACAATATAACTGCAACAATTAAACACTCTATCTATTATACTTG
ATCATAAAGATTTTTTTTTCTCAATATTTTATAATTTTATCTCAGCATTTCTCTCGTACA
TGCACTTTTTTTATTTTACATTTTATGGATAAATTATGGGTTTAGGTAGATTATTGTGTC
TTTAAAAGATGTTATGTTGATTTTTATTATTTCAAAAATCGATAACTGAAAGAAAAGATT
ATTAACATTTTAACTAAACATGATAAAAAGTACTATGAATTAAAGGATCAAGAAAAAATC
TAAATGTTATGTAGGATAAAAATTGCTTTTGCACAAATATTTGTAGAAGTTTTTTTGCAC
AAGAAAGAAAAGAATATAACATTCCTTTAGAGGAAAAATGAAAGAAAAAAAAATGATATA
TATATATATATATATTATACATAATTATTTTTT
>g4512.t3 Gene=g4512 Length=150
MHPMDFVNSMRKKGQLIMGIGHRVKSINNPDIRVKIIKEFVLENFPAKPLLEYALEVEKI
TTSKKPNLILNVDGVIATCFVDMLRNCGAFSSEEAQEYINIGAINSLFVLGRSIGFIGHY
MDQRRLKQGLYRHPWDDISYVLPEQYNCNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4512.t3 | CDD | cd06100 | CCL_ACL-C | 1 | 140 | 0 |
| 5 | g4512.t3 | Gene3D | G3DSA:1.10.230.10 | - | 2 | 83 | 0 |
| 2 | g4512.t3 | PANTHER | PTHR23118:SF0 | ATP-CITRATE SYNTHASE | 1 | 145 | 0 |
| 3 | g4512.t3 | PANTHER | PTHR23118 | ATP-CITRATE SYNTHASE | 1 | 145 | 0 |
| 1 | g4512.t3 | Pfam | PF00285 | Citrate synthase, C-terminal domain | 5 | 131 | 0 |
| 4 | g4512.t3 | SUPERFAMILY | SSF48256 | Citrate synthase | 5 | 143 | 0 |
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 |
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.
