General information for g4011.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pyruvate carboxylase, mitochondrial.
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.t7 | isoform | g4011.t7 | 29513545 | 29515200 |
| chr_3 | g4011 | g4011.t7 | exon | g4011.t7.exon1 | 29513545 | 29514292 |
| chr_3 | g4011 | g4011.t7 | cds | g4011.t7.CDS1 | 29513657 | 29514292 |
| chr_3 | g4011 | g4011.t7 | exon | g4011.t7.exon2 | 29514346 | 29514374 |
| chr_3 | g4011 | g4011.t7 | cds | g4011.t7.CDS2 | 29514346 | 29514374 |
| chr_3 | g4011 | g4011.t7 | exon | g4011.t7.exon3 | 29514433 | 29514613 |
| chr_3 | g4011 | g4011.t7 | cds | g4011.t7.CDS3 | 29514433 | 29514613 |
| chr_3 | g4011 | g4011.t7 | exon | g4011.t7.exon4 | 29514677 | 29515028 |
| chr_3 | g4011 | g4011.t7 | cds | g4011.t7.CDS4 | 29514677 | 29515028 |
| chr_3 | g4011 | g4011.t7 | exon | g4011.t7.exon5 | 29515088 | 29515200 |
| chr_3 | g4011 | g4011.t7 | cds | g4011.t7.CDS5 | 29515088 | 29515200 |
| chr_3 | g4011 | g4011.t7 | TTS | g4011.t7 | 29515436 | 29515436 |
| chr_3 | g4011 | g4011.t7 | TSS | g4011.t7 | NA | NA |
Sequences
>g4011.t7 Gene=g4011 Length=1423
TTATACTGGTGATGTGAGCGATGCAAGCAAGACAAAATACAATTTAAAATACTATACTGA
TTTATCAGATGAATTAGTCAAAGCTGGAACTCATGTTTTAGCAATTAAAGATATGGCTGG
TTTATTGAAACCTCAAGCTGCTGGAATGCTTATCGATGCAATAAGACAGAGACATCCAGA
TGTTCCAATTCATATTCATACTCACGATACTAGTGGTGCTGGAGTTGCATCTATGTTAGA
ATGTGCTAAAGCAGGTGCTGATGTTGTCGATGTCGCTGTTGATTCAATGTCAGGAATGAC
TTCACAACCAAGCATGGGAGCAGTAGTGGCTTCATTGCAAGGCACTCCACTTGATACTGG
TTATCAGTTGAATGATATTTCTGAATATTCTGCATATTGGGAAGCAACTAGAACATTATA
TGCTCCATTCGAATGCACAACGACAATGAAATCAGGCAATGCTGATGTTTATCTTAATGA
AATTCCTGGTGGACAATATACAAACTTACAATTCCAAGCATTCTCGCTTGGACTCGGAGA
TTTCTTTGAAGATGTTAAGAAAGCATATCGTGAAGCAAATTTGTTACTTGGAGATATTAT
CAAAGTTACACCATCGTCGAAAGTTGTAGGTGATTTGGCACAATTTATGGTCCAAAATAA
ACTCACTGCTCAACAAGTACTCGATCGTGCTGAAGAATTATCATTTCCTAAATCAGTTAT
TGAATTCTTACAAGGTGCAATTGGAATTCCATATGGTGGATTTCCAGAACCATTCAGGAG
CAAAGTTTTGAAAGATATGCCACGTGTTGAAGGTCGACCAGGTGAATCTCTGCCACCACT
TGATTTTGATAAATTAAAGAAAGATATTCTTGAGAGTCATCCACATGCAACTGATCGTGA
TGTTATGTCTGCTGCATTATATCCACAAGTTACTAATGATTTCCTTACGTTCCGCGAGGA
ATATGGACCAGTCGACAAACTTGATACAAGAATTTTCCTTGTTGGACCTAAAGTCGGTGA
AGAATTCGAAGTTACATTAGAAAGAGGAAAGACATTACACATCAAGACACTTGCAATGGC
TGAAGATCTAACACCAAATGGCGAGAAAGAAATTTTCTTTGAATTGAATGGACAATTGAG
ATCAGTTTTCATTCGTGATAGTGAGGCATCTAAAGAATTACACATTCATCCAAAAGCTGT
GAAAGGAAATAAGAATGAAGTAGGTGCACCAATGCCTGGTAATGTCATTGATATTCGTGT
AAAGGTTGGAGATCATGTTGAGAAAGGTCAACCACTTGTCGTTCTTTCAGCAATGAAAAT
GGAAATGGTTGTTCAATCTCCGCGTGCTGGTACTGTTAAAACTTTGAGTATTCAACCTGG
AATGAAACTTGAAGGAGAGGATCTCATTCTCACTTTCGAATAA
>g4011.t7 Gene=g4011 Length=436
MAGLLKPQAAGMLIDAIRQRHPDVPIHIHTHDTSGAGVASMLECAKAGADVVDVAVDSMS
GMTSQPSMGAVVASLQGTPLDTGYQLNDISEYSAYWEATRTLYAPFECTTTMKSGNADVY
LNEIPGGQYTNLQFQAFSLGLGDFFEDVKKAYREANLLLGDIIKVTPSSKVVGDLAQFMV
QNKLTAQQVLDRAEELSFPKSVIEFLQGAIGIPYGGFPEPFRSKVLKDMPRVEGRPGESL
PPLDFDKLKKDILESHPHATDRDVMSAALYPQVTNDFLTFREEYGPVDKLDTRIFLVGPK
VGEEFEVTLERGKTLHIKTLAMAEDLTPNGEKEIFFELNGQLRSVFIRDSEASKELHIHP
KAVKGNKNEVGAPMPGNVIDIRVKVGDHVEKGQPLVVLSAMKMEMVVQSPRAGTVKTLSI
QPGMKLEGEDLILTFE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4011.t7 | CDD | cd06850 | biotinyl_domain | 369 | 435 | 2.71842E-26 |
| 12 | g4011.t7 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 1 | 107 | 6.4E-40 |
| 10 | g4011.t7 | Gene3D | G3DSA:1.10.472.90 | - | 108 | 227 | 2.6E-61 |
| 11 | g4011.t7 | Gene3D | G3DSA:1.10.10.60 | - | 234 | 286 | 3.2E-19 |
| 13 | g4011.t7 | Gene3D | G3DSA:3.10.600.10 | pyruvate carboxylase f1077a mutant domain | 291 | 355 | 7.8E-18 |
| 9 | g4011.t7 | Gene3D | G3DSA:2.40.50.100 | - | 359 | 436 | 1.3E-22 |
| 4 | g4011.t7 | PANTHER | PTHR43778 | PYRUVATE CARBOXYLASE | 1 | 434 | 8.8E-195 |
| 1 | g4011.t7 | Pfam | PF00682 | HMGL-like | 1 | 94 | 2.2E-17 |
| 2 | g4011.t7 | Pfam | PF02436 | Conserved carboxylase domain | 119 | 318 | 1.6E-70 |
| 3 | g4011.t7 | Pfam | PF00364 | Biotin-requiring enzyme | 369 | 434 | 2.1E-19 |
| 8 | g4011.t7 | ProSitePatterns | PS00188 | Biotin-requiring enzymes attachment site. | 392 | 409 | - |
| 15 | g4011.t7 | ProSiteProfiles | PS50991 | Pyruvate carboxyltransferase domain. | 1 | 90 | 22.952 |
| 14 | g4011.t7 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 367 | 436 | 23.141 |
| 5 | g4011.t7 | SUPERFAMILY | SSF51569 | Aldolase | 1 | 127 | 1.78E-28 |
| 7 | g4011.t7 | SUPERFAMILY | SSF89000 | post-HMGL domain-like | 124 | 299 | 3.92E-51 |
| 6 | g4011.t7 | SUPERFAMILY | SSF51230 | Single hybrid motif | 357 | 436 | 3.14E-20 |
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:0003824 | catalytic activity | 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.
