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.t22 isoform g1576.t22 11964183 11969410
chr_3 g1576 g1576.t22 exon g1576.t22.exon1 11964183 11964464
chr_3 g1576 g1576.t22 cds g1576.t22.CDS1 11964219 11964464
chr_3 g1576 g1576.t22 exon g1576.t22.exon2 11967614 11967992
chr_3 g1576 g1576.t22 cds g1576.t22.CDS2 11967614 11967992
chr_3 g1576 g1576.t22 exon g1576.t22.exon3 11968063 11968550
chr_3 g1576 g1576.t22 cds g1576.t22.CDS3 11968063 11968550
chr_3 g1576 g1576.t22 exon g1576.t22.exon4 11968609 11968962
chr_3 g1576 g1576.t22 cds g1576.t22.CDS4 11968609 11968623
chr_3 g1576 g1576.t22 exon g1576.t22.exon5 11969024 11969118
chr_3 g1576 g1576.t22 exon g1576.t22.exon6 11969180 11969410
chr_3 g1576 g1576.t22 TTS g1576.t22 11969767 11969767
chr_3 g1576 g1576.t22 TSS g1576.t22 NA NA

Sequences

>g1576.t22 Gene=g1576 Length=1829
GTCGCAACGGAAAATGGAAATGAAAATCACGATGTAATGAGCAATAGTGAGCGCTTCAAA
TATAAAACGCAAACGAATGAAAATTTTCTCAGTCAGAATCAAACAACGGAGCCGAACACA
TCGTTCGTAGAAAAAATTACAATTCTTTCACCATTTGGATTGAATACTAAATCAAACATT
ATGAGTGAAAGCCGAGATAGACTTGGACAATGGCCTGTGGAATCAGAAGCTGAACTTACA
GGACAAGGATTGCAACGTTTGAAAAATAATCATTATAATAAGGGCCTTGCTTTCACTCAT
GAAGAACGACAAATTTTGGGAATTCATGGTTTGCTTGCACCAGGCATTAAATCTATTGAT
GAACAAATTAAGCATGCCCATATTTTATTGGAACGATGTGCGACTGATTTAGACAAATAT
ATTTATTTGATGGGACTTCAAGACCGCAATGTGAATTTATTTTATCGCGTTCTTGCATCC
GATATTGCAAACATGATGCCTTTAGTTTATACACCAACTGTTGGTCTTGCATGTCAAAAG
TATTCGATGATTTACACTAATCCTAAGGGTCTTTACATATCAATTTATGATAAGGGTCAT
ATTTACGATGTCATCAAAAATTGGCCAGAATTTGATGTAAGAGCTATTGTTGTTACTGAC
GGAGAAAGAATTTTAGGTTTGGGCGATCTTGGAGCTAACGGAATGGGTATTCCAGTTGGA
AAATTGGCACTCTACACTGCACTTGCTGGAATCAAACCTCATCAATGTTTACCAATCACA
CTCGATGTTGGCACAAATACTCAATCAATTCTTGATGATCCTCTTTATATAGGATTGCGT
CAAAAACGTGTAACTGGACAAGAATATGATGACTTTATTGAGGAATTTATGCAAGCTGCT
GTTCGACGCTTCGGCCAAAGTTGTCTCATTCAATTTGAGGACTTTGGCAATTCAAACGCT
TTTAGACTTATTGAAAAATATCGCGAAGATTATTGCACTTTTAACGACGATATTCAGGGT
ACAGCTGCTGTAGCAGTTGCTGGCTTGCTTGCTTCACTTCGAGTCACTAAAACTCGTTTA
TCAGATAATAAAATTTTGTTCCAAGGTAGCGGCGAAGCTGCACTCGGAATTGCTGAATTA
TGTGTCATGATAGTAAAGGATTGATTGTCAAAGATCGTCCAAAAGGTGGACTCAACCATC
ATAAGAGTAAATTTGCTCACGCTCATCACCCAGTTGATACATTAGCAGAAGCTGTAGATA
TTTTGAAACCAACAGTCTTGATTGGTGCTGCTGCAATTGGTGGAGCTTTTACACCCGAAA
TTATCAAAGCAATGGCTAGTTTTAATGAACGCCCAATTATTTTTGCTTTGTCAAATCCAA
CAAGCAAGGCTGAATGTACTGCTGAGGATGCATATATTCATAGCGATGGAAAAGCTGTTT
TTGCTTCTGGGTCACCTTTTGCGCCGGTCACTTACAAAGGACAAAAATTCTATCCAGGAC
AAGGCAATAATTCTTATATTTTCCCTGGTGTTGCACTTGGTGTCATTGCTGGTGCCGTTT
CCAAAATTCCAGAAGATATCTTTTTGATTTCCGCTAAAGCTCTTGCTGATTTAGTTACTG
ATGATGATTTAAATAAAGGAGCTTTATATCCACCATTAGAAACAATTCAAGATTGTTCAT
TTGAAATTGCTGTTAAAGTTATGGAATATGCTTATGATAATGGATTGGCTACGGTTCGTC
CTAAACCAAAAAATATGCGTACTTTCATCAAGGCCCAAATGTATGACCCATCTTACAAAC
CAGCCATCCCACCCGTATATAAATTATAA

>g1576.t22 Gene=g1576 Length=375
MSNSERFKYKTQTNENFLSQNQTTEPNTSFVEKITILSPFGLNTKSNIMSESRDRLGQWP
VESEAELTGQGLQRLKNNHYNKGLAFTHEERQILGIHGLLAPGIKSIDEQIKHAHILLER
CATDLDKYIYLMGLQDRNVNLFYRVLASDIANMMPLVYTPTVGLACQKYSMIYTNPKGLY
ISIYDKGHIYDVIKNWPEFDVRAIVVTDGERILGLGDLGANGMGIPVGKLALYTALAGIK
PHQCLPITLDVGTNTQSILDDPLYIGLRQKRVTGQEYDDFIEEFMQAAVRRFGQSCLIQF
EDFGNSNAFRLIEKYREDYCTFNDDIQGTAAVAVAGLLASLRVTKTRLSDNKILFQGSGE
AALGIAELCVMIVKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1576.t22 Gene3D G3DSA:3.40.50.10380 - 71 323 1.2E-118
14 g1576.t22 Gene3D G3DSA:3.40.50.720 - 324 374 1.2E-16
18 g1576.t22 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
3 g1576.t22 PANTHER PTHR23406 MALIC ENZYME-RELATED 40 374 4.3E-169
4 g1576.t22 PANTHER PTHR23406:SF80 GH17657P-RELATED 40 374 4.3E-169
15 g1576.t22 PIRSF PIRSF000106 ME 13 375 5.3E-135
9 g1576.t22 PRINTS PR00072 Malic enzyme signature 141 165 3.2E-67
7 g1576.t22 PRINTS PR00072 Malic enzyme signature 201 230 3.2E-67
10 g1576.t22 PRINTS PR00072 Malic enzyme signature 237 259 3.2E-67
5 g1576.t22 PRINTS PR00072 Malic enzyme signature 297 315 3.2E-67
6 g1576.t22 PRINTS PR00072 Malic enzyme signature 322 338 3.2E-67
8 g1576.t22 PRINTS PR00072 Malic enzyme signature 353 369 3.2E-67
1 g1576.t22 Pfam PF00390 Malic enzyme, N-terminal domain 135 316 1.2E-78
2 g1576.t22 Pfam PF03949 Malic enzyme, NAD binding domain 326 372 9.0E-13
16 g1576.t22 ProSitePatterns PS00331 Malic enzymes signature. 322 338 -
17 g1576.t22 SMART SM01274 malic_2 135 316 4.5E-104
12 g1576.t22 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 65 325 7.19E-107
11 g1576.t22 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 326 373 3.69E-11

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

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.

Raw TPM values