General information for g4512.t13
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.t13 | isoform | g4512.t13 | 2951987 | 2954820 |
| chr_2 | g4512 | g4512.t13 | exon | g4512.t13.exon1 | 2951987 | 2952295 |
| chr_2 | g4512 | g4512.t13 | cds | g4512.t13.CDS1 | 2951988 | 2952295 |
| chr_2 | g4512 | g4512.t13 | exon | g4512.t13.exon2 | 2952359 | 2952891 |
| chr_2 | g4512 | g4512.t13 | cds | g4512.t13.CDS2 | 2952359 | 2952891 |
| chr_2 | g4512 | g4512.t13 | exon | g4512.t13.exon3 | 2952957 | 2953314 |
| chr_2 | g4512 | g4512.t13 | cds | g4512.t13.CDS3 | 2952957 | 2953314 |
| chr_2 | g4512 | g4512.t13 | exon | g4512.t13.exon4 | 2954655 | 2954820 |
| chr_2 | g4512 | g4512.t13 | cds | g4512.t13.CDS4 | 2954655 | 2954820 |
| chr_2 | g4512 | g4512.t13 | TSS | g4512.t13 | NA | NA |
| chr_2 | g4512 | g4512.t13 | TTS | g4512.t13 | NA | NA |
Sequences
>g4512.t13 Gene=g4512 Length=1366
ATGTCAGCTAAAGCGATTCGTGAGGTAACAGGAAAGGAACTTATAAACAAATATTTGGGT
GGTGTGAACGAAACTGGTGTTCAAAAAAGTCGTTTTGCTGCTGTCACCGAGAATACAGAT
TGGAGTCAATTGGTTGCTGAGAATCCATGGCTTGAAAGCACAGTAAATCAACTTATTAAG
CGTCGTGGGAAATTAGGATTGATTGCAGTCAATAAGAATTTTTCTCAAGTCAAGCAATGG
ATAAACGAGCGAATGGGAAAAGATCAAAAAGTTGGAAGTGCAGTTGGCAAACTCCGAAAT
TTCATTATTGAGCCATTTATACCTCACAAGGATGATGAGGAAGCATACGTTTGCATTTAT
TCACATCGAACGGCAGATACAATCTTATTTTATCATCAAGGTGGTGTTGACATTGGTGAC
GTCGATTCAAAGGCTCTTAAGCTCGATGTTCCTGTTGGAGCAACAGTCACAGTCGATGAT
ATTCAAAAAACCTTGTTAAAAGAAGTTGCAACAGCCAAAAAAGCACGTATTGGCAAATTT
ATTTATGAGCTTTATCAGTTATATTCTGATCTCTACTTTACATATCTTGAAATTAACCCT
CTCGTTGTCACTGATGACTCAATCTATATTTTGGATCTTGCTGCCAAAATTGATGCCACT
GCTGATTTTATTTGTCGTCCAAAATGGGGAGATATTGATTATCCGCCACCCTTTGGACGT
GATGCTTATCCCGAAGAAGCATATATTGCAGATTTGGATGCCAAATCTGGTGCATCTTTA
AAATTAACGATTTTAAATCGTAATGGTCGTATTTGGACTATGGTTGCTGGTGGTGGTGCA
AGTGTTATTTATTCAGATACTATTTGTGACTATGGTGGAGCTTCAGAATTGGCAAATTAT
GGCGAGTATAGTGGTGCACCTTCAGAACAACAAACTTACGAATATGCTAAAACTATTCTC
AATCTTATGACATCATCACCTAAACATCCTGATGGAAAAGTTTTGATTATTGGAGGTGGA
ATTGCAAATTTTACAAATGTTGCTGCAACATTCAGTGGAATCATTACTGCATTAAGAGAA
TTTATGGCTCGTTTGATTGAACATAAAGTCTCAGTTTTCGTTCGTCGTGCTGGTCCAAAT
TATCAAGAAGGTCTTCGTCGAATGCGTGAAATTGGTGCCACTCTTGGAATTCCTTTACAC
GTTTTCGGTCCAGAAACTCATATGACAGCAATTTGTGGAATGGCTCTTGGCAAAAAACCA
ATTCCTAATGTTGCTGATTTACACTTTGCAACAGCAAATTTCTTATTACCTGGTGGTCAA
CAACAGCAAGAACAACGTAAAATGATTTCTAGTCAAACATCTCAAA
>g4512.t13 Gene=g4512 Length=455
MSAKAIREVTGKELINKYLGGVNETGVQKSRFAAVTENTDWSQLVAENPWLESTVNQLIK
RRGKLGLIAVNKNFSQVKQWINERMGKDQKVGSAVGKLRNFIIEPFIPHKDDEEAYVCIY
SHRTADTILFYHQGGVDIGDVDSKALKLDVPVGATVTVDDIQKTLLKEVATAKKARIGKF
IYELYQLYSDLYFTYLEINPLVVTDDSIYILDLAAKIDATADFICRPKWGDIDYPPPFGR
DAYPEEAYIADLDAKSGASLKLTILNRNGRIWTMVAGGGASVIYSDTICDYGGASELANY
GEYSGAPSEQQTYEYAKTILNLMTSSPKHPDGKVLIIGGGIANFTNVAATFSGIITALRE
FMARLIEHKVSVFVRRAGPNYQEGLRRMREIGATLGIPLHVFGPETHMTAICGMALGKKP
IPNVADLHFATANFLLPGGQQQQEQRKMISSQTSQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4512.t13 | Gene3D | G3DSA:3.30.470.20 | - | 5 | 238 | 1.8E-92 |
| 8 | g4512.t13 | Gene3D | G3DSA:3.30.1490.20 | - | 32 | 106 | 1.8E-92 |
| 9 | g4512.t13 | Gene3D | G3DSA:3.40.50.261 | - | 242 | 404 | 8.1E-79 |
| 2 | g4512.t13 | PANTHER | PTHR23118 | ATP-CITRATE SYNTHASE | 1 | 438 | 5.6E-193 |
| 3 | g4512.t13 | PANTHER | PTHR23118:SF32 | ATP-CITRATE SYNTHASE | 1 | 438 | 5.6E-193 |
| 1 | g4512.t13 | Pfam | PF16114 | ATP citrate lyase citrate-binding | 240 | 418 | 4.6E-91 |
| 6 | g4512.t13 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 269 | 294 | - |
| 4 | g4512.t13 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 5 | 236 | 2.12E-31 |
| 5 | g4512.t13 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 258 | 394 | 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: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.
