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.t1 isoform g4011.t1 29505261 29515200
chr_3 g4011 g4011.t1 exon g4011.t1.exon1 29505261 29505411
chr_3 g4011 g4011.t1 cds g4011.t1.CDS1 29505261 29505411
chr_3 g4011 g4011.t1 exon g4011.t1.exon2 29505466 29505607
chr_3 g4011 g4011.t1 cds g4011.t1.CDS2 29505466 29505607
chr_3 g4011 g4011.t1 exon g4011.t1.exon3 29505673 29506213
chr_3 g4011 g4011.t1 cds g4011.t1.CDS3 29505673 29506213
chr_3 g4011 g4011.t1 exon g4011.t1.exon4 29509287 29509313
chr_3 g4011 g4011.t1 cds g4011.t1.CDS4 29509287 29509313
chr_3 g4011 g4011.t1 exon g4011.t1.exon5 29510641 29512153
chr_3 g4011 g4011.t1 cds g4011.t1.CDS5 29510641 29512153
chr_3 g4011 g4011.t1 exon g4011.t1.exon6 29512654 29512701
chr_3 g4011 g4011.t1 cds g4011.t1.CDS6 29512654 29512701
chr_3 g4011 g4011.t1 exon g4011.t1.exon7 29512921 29513318
chr_3 g4011 g4011.t1 cds g4011.t1.CDS7 29512921 29513318
chr_3 g4011 g4011.t1 exon g4011.t1.exon8 29513377 29513492
chr_3 g4011 g4011.t1 cds g4011.t1.CDS8 29513377 29513492
chr_3 g4011 g4011.t1 exon g4011.t1.exon9 29513545 29514292
chr_3 g4011 g4011.t1 cds g4011.t1.CDS9 29513545 29514292
chr_3 g4011 g4011.t1 exon g4011.t1.exon10 29514346 29514374
chr_3 g4011 g4011.t1 cds g4011.t1.CDS10 29514346 29514374
chr_3 g4011 g4011.t1 exon g4011.t1.exon11 29514433 29514613
chr_3 g4011 g4011.t1 cds g4011.t1.CDS11 29514433 29514613
chr_3 g4011 g4011.t1 exon g4011.t1.exon12 29514677 29515028
chr_3 g4011 g4011.t1 cds g4011.t1.CDS12 29514677 29515028
chr_3 g4011 g4011.t1 exon g4011.t1.exon13 29515088 29515200
chr_3 g4011 g4011.t1 cds g4011.t1.CDS13 29515088 29515200
chr_3 g4011 g4011.t1 TTS g4011.t1 29515436 29515436
chr_3 g4011 g4011.t1 TSS g4011.t1 NA NA

Sequences

>g4011.t1 Gene=g4011 Length=4359
ATGTTATTACAAATTTGTTTCTTTATTCTAATAGCCGTAGTACATGAAATTAATCCATTT
TTGGTTGTTCCTGCAACTTCTCCGACCCGTCATCAATTTATTGTAGGACTTGGTGTTCCT
CTAAATTTAGAAAATGAAGCAATTACTTATGGATGGACAATAAAAGCTCAATATTTTTTG
CCTGAATCAACTGCAGATGACCTTAAATTTGTTTATTTTCCCGGAATATTTAACAACGAT
AGTTGTTACACGTGTCCAAATTCAAAAGTTAAATTTGCAGTCAATACTGTAAATCAATAT
GTTGAAAATCAACAACATGTTTTCCCAAATGGCCGAAGAAGGAAGCGTGATATTTTAGTT
GATAATGATACAGGAAAATTTTATGAAATGTATGAACAAGAGGCACAAGAAGTTGGTAAT
GAAAATCTTAAATCGGATGACGATATATTTGACGACACTTTTGAGAAAGATGCACGTATG
AATCCAAAACTAAGTGACTACCCAAAACCAAATGAAGAAGAATTAGATGATTTAAGTGGC
ACAAGATGGCTATTATATGATACATTAGGAAAAATGTTGGAAGCAAAAGGTTTCGAAGGA
AGACACTGTATATTGAGAGCAATTTGTGAATCAGCAGAAACAAATTTTGGTTATCACAGT
GGCCTCTTTGGTCAGCTTTTTCATATTTTATTTACACCTTCAAGTACTGAAGACAAAATA
GTTAATAAAGATCATTATGATTATATTAAAGCGGAAACGATGGGAAAGGATGGTGAACAT
TGTGATAAAATTTTTTATCAATGTAAAAGATCTATAATGGAAATTTTTACTCAACAATTA
AAAAATAAATATTCAACACATGTCGAATATAAACCAATAAGATCAGTTTTGGTTGCTAAT
CGCGGTGAAATCGCGATAAGAGTGTTCAGAGCATGTAATGAAATGGGAATTCGATCTGTT
GCAATTTATTCTGAGCAAGACAAAATGCATATGCATCGACAGAAGGCTGATGAATCATAT
TTAGTCGGCAAAGGTTTGCCACCTGTTGAAGCATATCTAAACATTCCAGAAATTATTAGA
GTATGCAAAGAGAATGACGTTGATGCAATTCATCCTGGTTATGGTTTTCTGAGTGAGCGT
GCTGATTTTGCACAAGCAGTCACTGATGCAGGCATTCGCTTCATTGGACCGTCTCCAAAG
GTTGTTCAACAAATGGGAGATAAAGTTGCAGCACGTCAAGCGGCTATTGAAGCTAAAGTG
CCAATTGTTCCTGGTACAGATGGTCCAGTTCACACAAAAGAAGAAGCTGTTGAATTTTGT
AGAAAACATGGACTGCCTGTGATTTTTAAAGCTGCTTATGGTGGCGGTGGAAGAGGAATG
CGAGTTGTACGTAAAATGGAAGATGTAGAAGAATTATTCACAAGAGCAAGTTCTGAAGCA
AAAGCAGCTTTTGGAAATGGTGCAATGTTTATTGAGAAATTTATTGAACGTCCAAGACAC
ATTGAAGTTCAATTGCTCGGTGATAAAGCTGGAAATGTCGTCCATCTTTATGAACGTGAT
TGCTCTGTTCAACGTCGTCATCAGAAAGTTGTCGAAATTGCACCTGCTCCTCGTTTATCT
ACAGAAGTTCGTGATAGAATGACAGAATATGCCGTCAGATTAGCAAAACATGTCGGTTAT
GAAAATGCAGGAACAGTAGAATTTTTGTGTGATGAAAATGGAAATTTCTATTTCATTGAA
GTCAATGCAAGATTGCAAGTTGAGCATACAGTTACAGAAGAAGTCACACATATTGATTTA
GTTCAATCACAAATTAGAGTTGCTGAAGGAATGACATTACCTGAAATGGGTCTTACACAA
GAAAATATTACAACTCAAGGATATGCAATTCAATGTCGAGTCACAACAGAAGATCCAGCA
AATGATTTTCAACCAAGCGTTGGTCGTCTTGAAGTATTCAGAAGTGGTGAGGGTATGGGT
ATTCGTTTGGATTCAGCTTCAGCGTATGCTGGAGCAATTATTTCACCCTATTACGACTCG
TTGCTCGTAAAAATTATTTCACATGCTGCTGATCTTCAATCTTCAGCTGCTAAAATGACA
AGAGCTTTGAGAGAATTTAGAATTCGTGGTGTCAAAACAAATATTCCATTTTTAATGAAT
GTACTCGAAAATCAAAAGTTTTTGAATGGTGTTCTCGACACTTATTTTATTGATGAGCAT
CCACAGCTCTTTAAATTCCAACGTTCACAAAATCGTGCACAAAAGTTATTGAATTATCTT
GGACATGTTTTAGTTAATGGACCAAAGACTCCACTTGCAACTGGCCTAAAACCTGCTGAT
AATGTTCATCCACATGTTCCTGAAACTCCTTTGGACTTGTCTCCAGAGGCATTGGAACAA
GAAAAAAAAATAGGACGTAAAGTCAATGCGCCACCACCAGGATTGCGAGATATTTTTAAA
TCAGAAGGACCGGAAGCTTTTGCAAAAGCAGTTCGTGCAAAAAAAAATCTTTTGTTGATG
GATACAACTTTCCGTGATGCTCATCAATCTCTTTTGGCCACACGTGTTCGTACTCATGAT
TTATTGAAAATTTCACCTTTTGTTGCACACAAATTTAACAATTTATATTCACTTGAAAAT
TGGGGAGGAGCAACATTTGATGTTGCATTGAGATTTTTACATGAATGTCCATGGGAAAGA
TTAGAGGAAATGAGAAATAGAATTCCTAATATTCCTTTCCAAATGTTATTGCGAGGGGCT
AACGGTGTTGGTTATACAAATTATCCAGATAATGTTATTTATAAGTTCTGTGAACTTGCT
GTTCAATGTGGAATGGATATTTTCAGAGTTTTTGACAGTTTGAATTACTTGCCTAATTTA
ATTTTGGGAATGGAAGCTGCAGCTAAAGCTGGTGGTATTGTTGAGGCAACAATCAGTTAT
ACTGGTGATGTGAGCGATGCAAGCAAGACAAAATACAATTTAAAATACTATACTGATTTA
TCAGATGAATTAGTCAAAGCTGGAACTCATGTTTTAGCAATTAAAGATATGGCTGGTTTA
TTGAAACCTCAAGCTGCTGGAATGCTTATCGATGCAATAAGACAGAGACATCCAGATGTT
CCAATTCATATTCATACTCACGATACTAGTGGTGCTGGAGTTGCATCTATGTTAGAATGT
GCTAAAGCAGGTGCTGATGTTGTCGATGTCGCTGTTGATTCAATGTCAGGAATGACTTCA
CAACCAAGCATGGGAGCAGTAGTGGCTTCATTGCAAGGCACTCCACTTGATACTGGTTAT
CAGTTGAATGATATTTCTGAATATTCTGCATATTGGGAAGCAACTAGAACATTATATGCT
CCATTCGAATGCACAACGACAATGAAATCAGGCAATGCTGATGTTTATCTTAATGAAATT
CCTGGTGGACAATATACAAACTTACAATTCCAAGCATTCTCGCTTGGACTCGGAGATTTC
TTTGAAGATGTTAAGAAAGCATATCGTGAAGCAAATTTGTTACTTGGAGATATTATCAAA
GTTACACCATCGTCGAAAGTTGTAGGTGATTTGGCACAATTTATGGTCCAAAATAAACTC
ACTGCTCAACAAGTACTCGATCGTGCTGAAGAATTATCATTTCCTAAATCAGTTATTGAA
TTCTTACAAGGTGCAATTGGAATTCCATATGGTGGATTTCCAGAACCATTCAGGAGCAAA
GTTTTGAAAGATATGCCACGTGTTGAAGGTCGACCAGGTGAATCTCTGCCACCACTTGAT
TTTGATAAATTAAAGAAAGATATTCTTGAGAGTCATCCACATGCAACTGATCGTGATGTT
ATGTCTGCTGCATTATATCCACAAGTTACTAATGATTTCCTTACGTTCCGCGAGGAATAT
GGACCAGTCGACAAACTTGATACAAGAATTTTCCTTGTTGGACCTAAAGTCGGTGAAGAA
TTCGAAGTTACATTAGAAAGAGGAAAGACATTACACATCAAGACACTTGCAATGGCTGAA
GATCTAACACCAAATGGCGAGAAAGAAATTTTCTTTGAATTGAATGGACAATTGAGATCA
GTTTTCATTCGTGATAGTGAGGCATCTAAAGAATTACACATTCATCCAAAAGCTGTGAAA
GGAAATAAGAATGAAGTAGGTGCACCAATGCCTGGTAATGTCATTGATATTCGTGTAAAG
GTTGGAGATCATGTTGAGAAAGGTCAACCACTTGTCGTTCTTTCAGCAATGAAAATGGAA
ATGGTTGTTCAATCTCCGCGTGCTGGTACTGTTAAAACTTTGAGTATTCAACCTGGAATG
AAACTTGAAGGAGAGGATCTCATTCTCACTTTCGAATAA

>g4011.t1 Gene=g4011 Length=1452
MLLQICFFILIAVVHEINPFLVVPATSPTRHQFIVGLGVPLNLENEAITYGWTIKAQYFL
PESTADDLKFVYFPGIFNNDSCYTCPNSKVKFAVNTVNQYVENQQHVFPNGRRRKRDILV
DNDTGKFYEMYEQEAQEVGNENLKSDDDIFDDTFEKDARMNPKLSDYPKPNEEELDDLSG
TRWLLYDTLGKMLEAKGFEGRHCILRAICESAETNFGYHSGLFGQLFHILFTPSSTEDKI
VNKDHYDYIKAETMGKDGEHCDKIFYQCKRSIMEIFTQQLKNKYSTHVEYKPIRSVLVAN
RGEIAIRVFRACNEMGIRSVAIYSEQDKMHMHRQKADESYLVGKGLPPVEAYLNIPEIIR
VCKENDVDAIHPGYGFLSERADFAQAVTDAGIRFIGPSPKVVQQMGDKVAARQAAIEAKV
PIVPGTDGPVHTKEEAVEFCRKHGLPVIFKAAYGGGGRGMRVVRKMEDVEELFTRASSEA
KAAFGNGAMFIEKFIERPRHIEVQLLGDKAGNVVHLYERDCSVQRRHQKVVEIAPAPRLS
TEVRDRMTEYAVRLAKHVGYENAGTVEFLCDENGNFYFIEVNARLQVEHTVTEEVTHIDL
VQSQIRVAEGMTLPEMGLTQENITTQGYAIQCRVTTEDPANDFQPSVGRLEVFRSGEGMG
IRLDSASAYAGAIISPYYDSLLVKIISHAADLQSSAAKMTRALREFRIRGVKTNIPFLMN
VLENQKFLNGVLDTYFIDEHPQLFKFQRSQNRAQKLLNYLGHVLVNGPKTPLATGLKPAD
NVHPHVPETPLDLSPEALEQEKKIGRKVNAPPPGLRDIFKSEGPEAFAKAVRAKKNLLLM
DTTFRDAHQSLLATRVRTHDLLKISPFVAHKFNNLYSLENWGGATFDVALRFLHECPWER
LEEMRNRIPNIPFQMLLRGANGVGYTNYPDNVIYKFCELAVQCGMDIFRVFDSLNYLPNL
ILGMEAAAKAGGIVEATISYTGDVSDASKTKYNLKYYTDLSDELVKAGTHVLAIKDMAGL
LKPQAAGMLIDAIRQRHPDVPIHIHTHDTSGAGVASMLECAKAGADVVDVAVDSMSGMTS
QPSMGAVVASLQGTPLDTGYQLNDISEYSAYWEATRTLYAPFECTTTMKSGNADVYLNEI
PGGQYTNLQFQAFSLGLGDFFEDVKKAYREANLLLGDIIKVTPSSKVVGDLAQFMVQNKL
TAQQVLDRAEELSFPKSVIEFLQGAIGIPYGGFPEPFRSKVLKDMPRVEGRPGESLPPLD
FDKLKKDILESHPHATDRDVMSAALYPQVTNDFLTFREEYGPVDKLDTRIFLVGPKVGEE
FEVTLERGKTLHIKTLAMAEDLTPNGEKEIFFELNGQLRSVFIRDSEASKELHIHPKAVK
GNKNEVGAPMPGNVIDIRVKVGDHVEKGQPLVVLSAMKMEMVVQSPRAGTVKTLSIQPGM
KLEGEDLILTFE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
27 g4011.t1 CDD cd07937 DRE_TIM_PC_TC_5S 839 1122 3.24429E-159
28 g4011.t1 CDD cd06850 biotinyl_domain 1385 1451 8.15908E-27
17 g4011.t1 Gene3D G3DSA:3.30.470.130 - 280 746 5.1E-199
21 g4011.t1 Gene3D G3DSA:3.10.600.10 pyruvate carboxylase f1077a mutant domain 750 1365 2.2E-291
20 g4011.t1 Gene3D G3DSA:3.20.20.70 Aldolase class I 785 1122 2.2E-291
18 g4011.t1 Gene3D G3DSA:1.10.472.90 - 1123 1255 2.2E-291
19 g4011.t1 Gene3D G3DSA:1.10.10.60 - 1256 1301 2.2E-291
16 g4011.t1 Gene3D G3DSA:2.40.50.100 - 1375 1452 6.8E-22
8 g4011.t1 PANTHER PTHR43778 PYRUVATE CARBOXYLASE 289 1450 0.0
1 g4011.t1 Pfam PF07841 DM4/DM12 family 182 268 2.5E-23
7 g4011.t1 Pfam PF00289 Biotin carboxylase, N-terminal domain 293 401 1.5E-41
5 g4011.t1 Pfam PF02786 Carbamoyl-phosphate synthase L chain, ATP binding domain 407 615 1.2E-79
2 g4011.t1 Pfam PF02785 Biotin carboxylase C-terminal domain 631 739 1.9E-31
3 g4011.t1 Pfam PF00682 HMGL-like 839 1110 1.8E-29
4 g4011.t1 Pfam PF02436 Conserved carboxylase domain 1135 1334 1.5E-69
6 g4011.t1 Pfam PF00364 Biotin-requiring enzyme 1385 1450 1.0E-18
23 g4011.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
24 g4011.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
25 g4011.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
26 g4011.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
22 g4011.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 1452 -
29 g4011.t1 ProSitePatterns PS00867 Carbamoyl-phosphate synthase subdomain signature 2. 578 585 -
30 g4011.t1 ProSitePatterns PS00188 Biotin-requiring enzymes attachment site. 1408 1425 -
34 g4011.t1 ProSiteProfiles PS50979 Biotin carboxylation domain profile. 292 742 54.511
37 g4011.t1 ProSiteProfiles PS50975 ATP-grasp fold profile. 414 609 47.312
36 g4011.t1 ProSiteProfiles PS50991 Pyruvate carboxyltransferase domain. 837 1106 38.577
35 g4011.t1 ProSiteProfiles PS50968 Biotinyl/lipoyl domain profile. 1383 1452 23.141
31 g4011.t1 SMART SM00718 dm4_12 177 275 3.7E-24
32 g4011.t1 SMART SM00878 Biotin_carb_C_2 631 738 2.8E-48
9 g4011.t1 SUPERFAMILY SSF52440 PreATP-grasp domain 272 405 7.91E-46
11 g4011.t1 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like 375 643 1.4E-69
10 g4011.t1 SUPERFAMILY SSF51246 Rudiment single hybrid motif 626 744 3.71E-37
12 g4011.t1 SUPERFAMILY SSF51569 Aldolase 831 1143 2.2E-81
14 g4011.t1 SUPERFAMILY SSF89000 post-HMGL domain-like 1140 1315 3.33E-50
13 g4011.t1 SUPERFAMILY SSF51230 Single hybrid motif 1373 1452 1.7E-19
15 g4011.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 16 -
33 g4011.t1 TIGRFAM TIGR01235 pyruv_carbox: pyruvate carboxylase 295 1452 0.0

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:0004736 pyruvate carboxylase activity MF
GO:0046872 metal ion binding MF
GO:0006090 pyruvate metabolic process BP
GO:0005524 ATP binding MF
GO:0006094 gluconeogenesis BP
GO:0009374 biotin binding MF
GO:0003824 catalytic activity MF

KEGG

Orthology

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.

Raw TPM values