Gene loci information

Transcript annotation

  • This transcript has been annotated as Pyruvate carboxylase, mitochondrial.

Parent gene

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.t5 isoform g4011.t5 29506990 29511628
chr_3 g4011 g4011.t5 exon g4011.t5.exon1 29506990 29507059
chr_3 g4011 g4011.t5 TSS g4011.t5 29506993 29506993
chr_3 g4011 g4011.t5 exon g4011.t5.exon2 29509185 29509313
chr_3 g4011 g4011.t5 exon g4011.t5.exon3 29510641 29511628
chr_3 g4011 g4011.t5 cds g4011.t5.CDS1 29510722 29511627
chr_3 g4011 g4011.t5 TTS g4011.t5 NA NA

Sequences

>g4011.t5 Gene=g4011 Length=1187
GTTTAGTTCTGTTGCGGCTTTGAATCGTTTGAGTCGACGATCGGAAAATTTCTTATTAAA
TAAAAGTCTCATTGTTTTTAGTGTCAATTATTTAGAATTCAACAATGTCTATCTATACAG
CAAATAGTGGAATTCGAGCCATAAGGCATGCATCAAGAATTAGAATTTTTAGCAATTAAA
AAATAAATATTCAACACATGTCGAATATAAACCAATAAGATCAGTTTTGGTTGCTAATCG
CGGTGAAATCGCGATAAGAGTGTTCAGAGCATGTAATGAAATGGGAATTCGATCTGTTGC
AATTTATTCTGAGCAAGACAAAATGCATATGCATCGACAGAAGGCTGATGAATCATATTT
AGTCGGCAAAGGTTTGCCACCTGTTGAAGCATATCTAAACATTCCAGAAATTATTAGAGT
ATGCAAAGAGAATGACGTTGATGCAATTCATCCTGGTTATGGTTTTCTGAGTGAGCGTGC
TGATTTTGCACAAGCAGTCACTGATGCAGGCATTCGCTTCATTGGACCGTCTCCAAAGGT
TGTTCAACAAATGGGAGATAAAGTTGCAGCACGTCAAGCGGCTATTGAAGCTAAAGTGCC
AATTGTTCCTGGTACAGATGGTCCAGTTCACACAAAAGAAGAAGCTGTTGAATTTTGTAG
AAAACATGGACTGCCTGTGATTTTTAAAGCTGCTTATGGTGGCGGTGGAAGAGGAATGCG
AGTTGTACGTAAAATGGAAGATGTAGAAGAATTATTCACAAGAGCAAGTTCTGAAGCAAA
AGCAGCTTTTGGAAATGGTGCAATGTTTATTGAGAAATTTATTGAACGTCCAAGACACAT
TGAAGTTCAATTGCTCGGTGATAAAGCTGGAAATGTCGTCCATCTTTATGAACGTGATTG
CTCTGTTCAACGTCGTCATCAGAAAGTTGTCGAAATTGCACCTGCTCCTCGTTTATCTAC
AGAAGTTCGTGATAGAATGACAGAATATGCCGTCAGATTAGCAAAACATGTCGGTTATGA
AAATGCAGGAACAGTAGAATTTTTGTGTGATGAAAATGGAAATTTCTATTTCATTGAAGT
CAATGCAAGATTGCAAGTTGAGCATACAGTTACAGAAGAAGTCACACATATTGATTTAGT
TCAATCACAAATTAGAGTTGCTGAAGGAATGACATTACCTGAAATGG

>g4011.t5 Gene=g4011 Length=302
MGIRSVAIYSEQDKMHMHRQKADESYLVGKGLPPVEAYLNIPEIIRVCKENDVDAIHPGY
GFLSERADFAQAVTDAGIRFIGPSPKVVQQMGDKVAARQAAIEAKVPIVPGTDGPVHTKE
EAVEFCRKHGLPVIFKAAYGGGGRGMRVVRKMEDVEELFTRASSEAKAAFGNGAMFIEKF
IERPRHIEVQLLGDKAGNVVHLYERDCSVQRRHQKVVEIAPAPRLSTEVRDRMTEYAVRL
AKHVGYENAGTVEFLCDENGNFYFIEVNARLQVEHTVTEEVTHIDLVQSQIRVAEGMTLP
EM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4011.t5 Gene3D G3DSA:3.30.470.130 - 1 302 3.5E-138
3 g4011.t5 PANTHER PTHR43778 PYRUVATE CARBOXYLASE 2 301 7.6E-152
2 g4011.t5 Pfam PF00289 Biotin carboxylase, N-terminal domain 1 87 1.7E-29
1 g4011.t5 Pfam PF02786 Carbamoyl-phosphate synthase L chain, ATP binding domain 93 301 4.6E-81
6 g4011.t5 ProSitePatterns PS00867 Carbamoyl-phosphate synthase subdomain signature 2. 264 271 -
8 g4011.t5 ProSiteProfiles PS50979 Biotin carboxylation domain profile. 1 302 24.04
9 g4011.t5 ProSiteProfiles PS50975 ATP-grasp fold profile. 100 295 47.312
4 g4011.t5 SUPERFAMILY SSF52440 PreATP-grasp domain 1 93 2.3E-31
5 g4011.t5 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 61 301 3.54E-69

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. There were no conditions that were differentially expressed