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 g3335 g3335.t25 isoform g3335.t25 24725334 24727783
chr_3 g3335 g3335.t25 exon g3335.t25.exon1 24725334 24725466
chr_3 g3335 g3335.t25 cds g3335.t25.CDS1 24725462 24725466
chr_3 g3335 g3335.t25 exon g3335.t25.exon2 24725537 24725582
chr_3 g3335 g3335.t25 cds g3335.t25.CDS2 24725537 24725582
chr_3 g3335 g3335.t25 exon g3335.t25.exon3 24726089 24726166
chr_3 g3335 g3335.t25 cds g3335.t25.CDS3 24726089 24726166
chr_3 g3335 g3335.t25 exon g3335.t25.exon4 24726241 24726265
chr_3 g3335 g3335.t25 cds g3335.t25.CDS4 24726241 24726265
chr_3 g3335 g3335.t25 exon g3335.t25.exon5 24726323 24727558
chr_3 g3335 g3335.t25 cds g3335.t25.CDS5 24726323 24727558
chr_3 g3335 g3335.t25 exon g3335.t25.exon6 24727617 24727783
chr_3 g3335 g3335.t25 cds g3335.t25.CDS6 24727617 24727783
chr_3 g3335 g3335.t25 TTS g3335.t25 24727926 24727926
chr_3 g3335 g3335.t25 TSS g3335.t25 NA NA

Sequences

>g3335.t25 Gene=g3335 Length=1685
GAGATCCGCGTTTAAATAAAGGTCTTGCATTTTCACTTCAAGAACGTCAGGTATTAGGCA
TTCATGGTCTTCAACCAGCACGAATAAAGACTCAAGAAGAACAATTAGAGCTGTGTAAAA
TTTCAATTATGAGATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGACTTACAGG
ATCGAAATGAACGTCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGATGATGCCCA
TCATTTATACACCAACTGTTGGTTCAGCTTGCCAAAAATTCGGCTTAATTTATCGAAGAC
CAAGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAAAGAACT
GGCCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAGGTTTAG
GCGATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACACTGCCC
TTGCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAAATAATA
AAGATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAGGACAAG
CCTATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGACAAAATA
CTTTGATTCAATTTGAAGATTTTGGAAATCACAATGCTTTCAGGTTTTTAGACAAATACC
GTGACACTTATTGCACTTTTAATGATGATATTCAAGGCACAGCATCAGTTGCTGTTGCAG
GACTTCTTGCTTCAAAGCGTGTAACAGGAAAGAAATTGTCAGATAACAAAATTCTTTTCC
TCGGTGCTGGTGAAGCTGCTATCGGAATTGCCGATTTGTGTGTTAAGGCAATGATGACAG
AAGGAGTTTCACAAGATGAAGCGCGCGACAAGATTTGGATGGTTGATATTGATGGACTTT
TAGCAAAAGGACGACCAGAAGGGCAGTTAGGTGGTCACAAATGGTTTTATGCTAAAGAGC
ATGAAGTTATGAAAGATTTTACTGAAATTGTAAAAGAAGTAAGGCCATCAATTTTAATTG
GTGCAAGTGCTGTTGGTGGTGCTTTTACACCTGAAATTTTGCAAATGATGGCAGAATTCA
ATGAACGACCTATTATTTTTGCATTATCAAATCCAACAATTAAAGCTGAATATACTACAG
AAGCAGCTTATACACATACAAAAGGAAAATGCATTTTTGCTTCAGGTTCACCATTTGGTC
AAGTGAACTATAATGGACAAATTTTTAATCCTGGACAAGGAAATAATGCCTACATTTTTC
CTGGGGTCGCTTTAGGCGTTATTGCTACAGGCACTCATCATATTCCTGAAGACATGTTTT
TAATTGCAGCTGAAACAATTGCAAAACACGTATCAGATGAAGATATACAAAGAGGCTCAC
TATATCCACCACTTTCAGTCATTAAAGAATGCTCATTTGATATTGCTATTGGAATTACTA
AATACGCTTATGCCAAAGGTTTAGCAAGTTTGTATCCTGAGCCATCAGATAAGAAAACTT
GGTTGAAACAGCAACTTTATAATTTCAACTATGAAAGTTCAATGCCAATCACATGGCCTT
GGCCAGAAATGCCACACATTACCACCCGCCCTTTAGAACCTACTTTGCTTCATAAGAAAA
ATTAA

>g3335.t25 Gene=g3335 Length=518
MRYQEDLNKYQYLVDLQDRNERLFFRLVSENVEMMMPIIYTPTVGSACQKFGLIYRRPRG
LFVTFNDKGHVFDVLKNWPEPDVRAIVVTDGERILGLGDLGAQGMGIPVGKLALYTALAG
IKPHQCLPIVIDVGTNNKDLLEDPLYVGLRQPRVSGQAYDDFIDEFMEAVVKRYGQNTLI
QFEDFGNHNAFRFLDKYRDTYCTFNDDIQGTASVAVAGLLASKRVTGKKLSDNKILFLGA
GEAAIGIADLCVKAMMTEGVSQDEARDKIWMVDIDGLLAKGRPEGQLGGHKWFYAKEHEV
MKDFTEIVKEVRPSILIGASAVGGAFTPEILQMMAEFNERPIIFALSNPTIKAEYTTEAA
YTHTKGKCIFASGSPFGQVNYNGQIFNPGQGNNAYIFPGVALGVIATGTHHIPEDMFLIA
AETIAKHVSDEDIQRGSLYPPLSVIKECSFDIAIGITKYAYAKGLASLYPEPSDKKTWLK
QQLYNFNYESSMPITWPWPEMPHITTRPLEPTLLHKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g3335.t25 CDD cd05312 NAD_bind_1_malic_enz 208 485 7.77525E-146
17 g3335.t25 Gene3D G3DSA:1.20.1370.30 - 2 58 2.1E-249
14 g3335.t25 Gene3D G3DSA:3.40.50.10380 - 59 464 2.1E-249
15 g3335.t25 Gene3D G3DSA:3.40.50.720 - 206 392 2.1E-249
16 g3335.t25 Gene3D G3DSA:3.30.2330.30 - 465 500 2.1E-249
3 g3335.t25 PANTHER PTHR23406 MALIC ENZYME-RELATED 2 492 2.5E-240
4 g3335.t25 PANTHER PTHR23406:SF80 GH17657P-RELATED 2 492 2.5E-240
18 g3335.t25 PIRSF PIRSF000106 ME 1 494 6.2E-202
6 g3335.t25 PRINTS PR00072 Malic enzyme signature 23 47 8.9E-79
11 g3335.t25 PRINTS PR00072 Malic enzyme signature 83 112 8.9E-79
9 g3335.t25 PRINTS PR00072 Malic enzyme signature 119 141 8.9E-79
10 g3335.t25 PRINTS PR00072 Malic enzyme signature 179 197 8.9E-79
8 g3335.t25 PRINTS PR00072 Malic enzyme signature 204 220 8.9E-79
7 g3335.t25 PRINTS PR00072 Malic enzyme signature 235 251 8.9E-79
5 g3335.t25 PRINTS PR00072 Malic enzyme signature 338 354 8.9E-79
1 g3335.t25 Pfam PF00390 Malic enzyme, N-terminal domain 17 198 2.3E-80
2 g3335.t25 Pfam PF03949 Malic enzyme, NAD binding domain 208 461 2.1E-96
20 g3335.t25 ProSitePatterns PS00331 Malic enzymes signature. 204 220 -
21 g3335.t25 SMART SM01274 malic_2 17 198 4.8E-109
22 g3335.t25 SMART SM00919 Malic_M_2 208 461 1.8E-110
13 g3335.t25 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 3 207 3.6E-90
12 g3335.t25 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 208 502 6.36E-97

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