Gene loci information

Transcript annotation

  • This transcript has been annotated as NADP-dependent malic enzyme.

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 g1576 g1576.t20 isoform g1576.t20 11964183 11969113
chr_3 g1576 g1576.t20 exon g1576.t20.exon1 11964183 11964464
chr_3 g1576 g1576.t20 cds g1576.t20.CDS1 11964219 11964464
chr_3 g1576 g1576.t20 exon g1576.t20.exon2 11967614 11967992
chr_3 g1576 g1576.t20 cds g1576.t20.CDS2 11967614 11967992
chr_3 g1576 g1576.t20 exon g1576.t20.exon3 11968063 11968962
chr_3 g1576 g1576.t20 cds g1576.t20.CDS3 11968063 11968962
chr_3 g1576 g1576.t20 exon g1576.t20.exon4 11969024 11969113
chr_3 g1576 g1576.t20 cds g1576.t20.CDS4 11969024 11969112
chr_3 g1576 g1576.t20 TTS g1576.t20 11969767 11969767
chr_3 g1576 g1576.t20 TSS g1576.t20 NA NA

Sequences

>g1576.t20 Gene=g1576 Length=1651
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATAT
ATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCC
GATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAG
TATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCAT
ATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGAC
GGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGA
AAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACA
CTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGT
CAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCT
GTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCT
TTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGT
ACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTA
TCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTA
TGTGTCATGGCAATGATTAAAGAAGGTGTTTGTGAAGAAGACGCTCGCTCACGTGTATGG
CTTGTAGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCATCAT
AAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATTAGCAGAAGCTGTAGATATT
TTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGAAATT
ATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTTTGCTTTGTCAAATCCAACA
AGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAGCGATGGAAAAGCTGTTTTT
GCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACAAAAATTCTATCCAGGACAA
GGCAATAATTCTTATATTTTCCCTGGTGTTGCACTTGGTGTCATTGCTGGTGCCGTTTCC
AAAATTCCAGAAGATATCTTTTTGATTTCCG

>g1576.t20 Gene=g1576 Length=538
MSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKITILSPFGLNTKSNIMSESRDRLGQWP
VESEAELTGQGLQRLKNNHYNKGLAFTHEERQILGIHGLLAPGIKSIDEQIKHAHILLER
CATDLDKYIYLMGLQDRNVNLFYRVLASDIANMMPLVYTPTVGLACQKYSMIYTNPKGLY
ISIYDKGHIYDVIKNWPEFDVRAIVVTDGERILGLGDLGANGMGIPVGKLALYTALAGIK
PHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIEEFMQAAVRRFGQSCLIQF
EDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLRVTKTRLSDNKILFQGSGE
AALGIAELCVMAMIKEGVCEEDARSRVWLVDSKGLIVKDRPKGGLNHHKSKFAHAHHPVD
TLAEAVDILKPTVLIGAAAIGGAFTPEIIKAMASFNERPIIFALSNPTSKAECTAEDAYI
HSDGKAVFASGSPFAPVTYKGQKFYPGQGNNSYIFPGVALGVIAGAVSKIPEDIFLIS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g1576.t20 Gene3D G3DSA:1.20.1370.30 - 70 176 2.8E-226
14 g1576.t20 Gene3D G3DSA:3.40.50.10380 - 177 537 2.8E-226
15 g1576.t20 Gene3D G3DSA:3.40.50.720 - 324 510 2.8E-226
21 g1576.t20 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
3 g1576.t20 PANTHER PTHR23406 MALIC ENZYME-RELATED 40 538 2.1E-260
4 g1576.t20 PANTHER PTHR23406:SF80 GH17657P-RELATED 40 538 2.1E-260
17 g1576.t20 PIRSF PIRSF000106 ME 16 538 4.6E-201
10 g1576.t20 PRINTS PR00072 Malic enzyme signature 141 165 6.4E-77
7 g1576.t20 PRINTS PR00072 Malic enzyme signature 201 230 6.4E-77
11 g1576.t20 PRINTS PR00072 Malic enzyme signature 237 259 6.4E-77
5 g1576.t20 PRINTS PR00072 Malic enzyme signature 297 315 6.4E-77
6 g1576.t20 PRINTS PR00072 Malic enzyme signature 322 338 6.4E-77
9 g1576.t20 PRINTS PR00072 Malic enzyme signature 353 369 6.4E-77
8 g1576.t20 PRINTS PR00072 Malic enzyme signature 456 472 6.4E-77
1 g1576.t20 Pfam PF00390 Malic enzyme, N-terminal domain 135 316 2.8E-78
2 g1576.t20 Pfam PF03949 Malic enzyme, NAD binding domain 326 537 1.6E-82
18 g1576.t20 ProSitePatterns PS00331 Malic enzymes signature. 322 338 -
19 g1576.t20 SMART SM01274 malic_2 135 316 4.5E-104
20 g1576.t20 SMART SM00919 Malic_M_2 326 537 1.0E-81
13 g1576.t20 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 65 325 2.01E-106
12 g1576.t20 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 326 536 1.75E-78

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:0004471 malate dehydrogenase (decarboxylating) (NAD+) activity MF
GO:0004470 malic enzyme activity MF
GO:0051287 NAD binding MF
GO:0055114 NA NA

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