General information for g4011.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pyruvate carboxylase 1.
Parent gene
- The parent gene g4011 is located on chr_3: 29513545..29515200 (+ 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_3 | g4011 | g4011.t6 | isoform | g4011.t6 | 29506990 | 29512153 |
| chr_3 | g4011 | g4011.t6 | exon | g4011.t6.exon1 | 29506990 | 29507074 |
| chr_3 | g4011 | g4011.t6 | TSS | g4011.t6 | 29506993 | 29506993 |
| chr_3 | g4011 | g4011.t6 | exon | g4011.t6.exon2 | 29509185 | 29509313 |
| chr_3 | g4011 | g4011.t6 | exon | g4011.t6.exon3 | 29510641 | 29512153 |
| chr_3 | g4011 | g4011.t6 | cds | g4011.t6.CDS1 | 29510722 | 29512152 |
| chr_3 | g4011 | g4011.t6 | TTS | g4011.t6 | NA | NA |
Sequences
>g4011.t6 Gene=g4011 Length=1727
GTTTAGTTCTGTTGCGGCTTTGAATCGTTTGAGTCGACGATCGGAAAATTTCTTATTAAA
TAAAAGTCTCGTGCGTCTTAGATTTATTGTTTTTAGTGTCAATTATTTAGAATTCAACAA
TGTCTATCTATACAGCAAATAGTGGAATTCGAGCCATAAGGCATGCATCAAGAATTAGAA
TTTTTAGCAATTAAAAAATAAATATTCAACACATGTCGAATATAAACCAATAAGATCAGT
TTTGGTTGCTAATCGCGGTGAAATCGCGATAAGAGTGTTCAGAGCATGTAATGAAATGGG
AATTCGATCTGTTGCAATTTATTCTGAGCAAGACAAAATGCATATGCATCGACAGAAGGC
TGATGAATCATATTTAGTCGGCAAAGGTTTGCCACCTGTTGAAGCATATCTAAACATTCC
AGAAATTATTAGAGTATGCAAAGAGAATGACGTTGATGCAATTCATCCTGGTTATGGTTT
TCTGAGTGAGCGTGCTGATTTTGCACAAGCAGTCACTGATGCAGGCATTCGCTTCATTGG
ACCGTCTCCAAAGGTTGTTCAACAAATGGGAGATAAAGTTGCAGCACGTCAAGCGGCTAT
TGAAGCTAAAGTGCCAATTGTTCCTGGTACAGATGGTCCAGTTCACACAAAAGAAGAAGC
TGTTGAATTTTGTAGAAAACATGGACTGCCTGTGATTTTTAAAGCTGCTTATGGTGGCGG
TGGAAGAGGAATGCGAGTTGTACGTAAAATGGAAGATGTAGAAGAATTATTCACAAGAGC
AAGTTCTGAAGCAAAAGCAGCTTTTGGAAATGGTGCAATGTTTATTGAGAAATTTATTGA
ACGTCCAAGACACATTGAAGTTCAATTGCTCGGTGATAAAGCTGGAAATGTCGTCCATCT
TTATGAACGTGATTGCTCTGTTCAACGTCGTCATCAGAAAGTTGTCGAAATTGCACCTGC
TCCTCGTTTATCTACAGAAGTTCGTGATAGAATGACAGAATATGCCGTCAGATTAGCAAA
ACATGTCGGTTATGAAAATGCAGGAACAGTAGAATTTTTGTGTGATGAAAATGGAAATTT
CTATTTCATTGAAGTCAATGCAAGATTGCAAGTTGAGCATACAGTTACAGAAGAAGTCAC
ACATATTGATTTAGTTCAATCACAAATTAGAGTTGCTGAAGGAATGACATTACCTGAAAT
GGGTCTTACACAAGAAAATATTACAACTCAAGGATATGCAATTCAATGTCGAGTCACAAC
AGAAGATCCAGCAAATGATTTTCAACCAAGCGTTGGTCGTCTTGAAGTATTCAGAAGTGG
TGAGGGTATGGGTATTCGTTTGGATTCAGCTTCAGCGTATGCTGGAGCAATTATTTCACC
CTATTACGACTCGTTGCTCGTAAAAATTATTTCACATGCTGCTGATCTTCAATCTTCAGC
TGCTAAAATGACAAGAGCTTTGAGAGAATTTAGAATTCGTGGTGTCAAAACAAATATTCC
ATTTTTAATGAATGTACTCGAAAATCAAAAGTTTTTGAATGGTGTTCTCGACACTTATTT
TATTGATGAGCATCCACAGCTCTTTAAATTCCAACGTTCACAAAATCGTGCACAAAAGTT
ATTGAATTATCTTGGACATGTTTTAGTTAATGGACCAAAGACTCCACTTGCAACTGGCCT
AAAACCTGCTGATAATGTTCATCCACATGTTCCTGAAACTCCTTTGG
>g4011.t6 Gene=g4011 Length=477
MGIRSVAIYSEQDKMHMHRQKADESYLVGKGLPPVEAYLNIPEIIRVCKENDVDAIHPGY
GFLSERADFAQAVTDAGIRFIGPSPKVVQQMGDKVAARQAAIEAKVPIVPGTDGPVHTKE
EAVEFCRKHGLPVIFKAAYGGGGRGMRVVRKMEDVEELFTRASSEAKAAFGNGAMFIEKF
IERPRHIEVQLLGDKAGNVVHLYERDCSVQRRHQKVVEIAPAPRLSTEVRDRMTEYAVRL
AKHVGYENAGTVEFLCDENGNFYFIEVNARLQVEHTVTEEVTHIDLVQSQIRVAEGMTLP
EMGLTQENITTQGYAIQCRVTTEDPANDFQPSVGRLEVFRSGEGMGIRLDSASAYAGAII
SPYYDSLLVKIISHAADLQSSAAKMTRALREFRIRGVKTNIPFLMNVLENQKFLNGVLDT
YFIDEHPQLFKFQRSQNRAQKLLNYLGHVLVNGPKTPLATGLKPADNVHPHVPETPL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g4011.t6 | Gene3D | G3DSA:3.30.470.130 | - | 1 | 432 | 2.0E-185 |
| 11 | g4011.t6 | Gene3D | G3DSA:3.10.600.10 | pyruvate carboxylase f1077a mutant domain | 436 | 475 | 1.9E-8 |
| 4 | g4011.t6 | PANTHER | PTHR43778 | PYRUVATE CARBOXYLASE | 2 | 476 | 2.0E-231 |
| 3 | g4011.t6 | Pfam | PF00289 | Biotin carboxylase, N-terminal domain | 1 | 87 | 3.8E-29 |
| 2 | g4011.t6 | Pfam | PF02786 | Carbamoyl-phosphate synthase L chain, ATP binding domain | 93 | 301 | 1.6E-80 |
| 1 | g4011.t6 | Pfam | PF02785 | Biotin carboxylase C-terminal domain | 317 | 425 | 3.8E-32 |
| 9 | g4011.t6 | ProSitePatterns | PS00867 | Carbamoyl-phosphate synthase subdomain signature 2. | 264 | 271 | - |
| 12 | g4011.t6 | ProSiteProfiles | PS50979 | Biotin carboxylation domain profile. | 1 | 428 | 48.047 |
| 13 | g4011.t6 | ProSiteProfiles | PS50975 | ATP-grasp fold profile. | 100 | 295 | 47.312 |
| 8 | g4011.t6 | SMART | SM00878 | Biotin_carb_C_2 | 317 | 424 | 2.8E-48 |
| 5 | g4011.t6 | SUPERFAMILY | SSF52440 | PreATP-grasp domain | 1 | 93 | 5.28E-31 |
| 7 | g4011.t6 | SUPERFAMILY | SSF56059 | Glutathione synthetase ATP-binding domain-like | 61 | 329 | 1.36E-70 |
| 6 | g4011.t6 | SUPERFAMILY | SSF51246 | Rudiment single hybrid motif | 312 | 430 | 6.8E-38 |
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.
