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.t29 isoform g3335.t29 24726322 24727783
chr_3 g3335 g3335.t29 exon g3335.t29.exon1 24726322 24727558
chr_3 g3335 g3335.t29 cds g3335.t29.CDS1 24726481 24727558
chr_3 g3335 g3335.t29 exon g3335.t29.exon2 24727617 24727783
chr_3 g3335 g3335.t29 cds g3335.t29.CDS2 24727617 24727783
chr_3 g3335 g3335.t29 TTS g3335.t29 24727926 24727926
chr_3 g3335 g3335.t29 TSS g3335.t29 NA NA

Sequences

>g3335.t29 Gene=g3335 Length=1404
GGCTTAATTTATCGAAGACCAAGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTG
TTTGATGTATTAAAGAACTGGCCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGT
GAACGTATTTTAGGTTTAGGCGATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAA
CTGGCACTCTACACTGCCCTTGCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATC
GATGTGGGAACAAATAATAAAGATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAA
CCTAGAGTATCAGGACAAGCCTATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTT
AAACGTTATGGACAAAATACTTTGATTCAATTTGAAGATTTTGGAAATCACAATGCTTTC
AGGTTTTTAGACAAATACCGTGACACTTATTGCACTTTTAATGATGATATTCAAGGCACA
GCATCAGTTGCTGTTGCAGGACTTCTTGCTTCAAAGCGTGTAACAGGAAAGAAATTGTCA
GATAACAAAATTCTTTTCCTCGGTGCTGGTGAAGCTGCTATCGGAATTGCCGATTTGTGT
GTTAAGGCAATGATGACAGAAGGAGTTTCACAAGATGAAGCGCGCGACAAGATTTGGATG
GTTGATATTGATGGACTTTTAGCAAAAGGACGACCAGAAGGGCAGTTAGGTGGTCACAAA
TGGTTTTATGCTAAAGAGCATGAAGTTATGAAAGATTTTACTGAAATTGTAAAAGAAGTA
AGGCCATCAATTTTAATTGGTGCAAGTGCTGTTGGTGGTGCTTTTACACCTGAAATTTTG
CAAATGATGGCAGAATTCAATGAACGACCTATTATTTTTGCATTATCAAATCCAACAATT
AAAGCTGAATATACTACAGAAGCAGCTTATACACATACAAAAGGAAAATGCATTTTTGCT
TCAGGTTCACCATTTGGTCAAGTGAACTATAATGGACAAATTTTTAATCCTGGACAAGGA
AATAATGCCTACATTTTTCCTGGGGTCGCTTTAGGCGTTATTGCTACAGGCACTCATCAT
ATTCCTGAAGACATGTTTTTAATTGCAGCTGAAACAATTGCAAAACACGTATCAGATGAA
GATATACAAAGAGGCTCACTATATCCACCACTTTCAGTCATTAAAGAATGCTCATTTGAT
ATTGCTATTGGAATTACTAAATACGCTTATGCCAAAGGTTTAGCAAGTTTGTATCCTGAG
CCATCAGATAAGAAAACTTGGTTGAAACAGCAACTTTATAATTTCAACTATGAAAGTTCA
ATGCCAATCACATGGCCTTGGCCAGAAATGCCACACATTACCACCCGCCCTTTAGAACCT
ACTTTGCTTCATAAGAAAAATTAA

>g3335.t29 Gene=g3335 Length=414
MGIPVGKLALYTALAGIKPHQCLPIVIDVGTNNKDLLEDPLYVGLRQPRVSGQAYDDFID
EFMEAVVKRYGQNTLIQFEDFGNHNAFRFLDKYRDTYCTFNDDIQGTASVAVAGLLASKR
VTGKKLSDNKILFLGAGEAAIGIADLCVKAMMTEGVSQDEARDKIWMVDIDGLLAKGRPE
GQLGGHKWFYAKEHEVMKDFTEIVKEVRPSILIGASAVGGAFTPEILQMMAEFNERPIIF
ALSNPTIKAEYTTEAAYTHTKGKCIFASGSPFGQVNYNGQIFNPGQGNNAYIFPGVALGV
IATGTHHIPEDMFLIAAETIAKHVSDEDIQRGSLYPPLSVIKECSFDIAIGITKYAYAKG
LASLYPEPSDKKTWLKQQLYNFNYESSMPITWPWPEMPHITTRPLEPTLLHKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3335.t29 CDD cd05312 NAD_bind_1_malic_enz 104 381 3.47732E-146
12 g3335.t29 Gene3D G3DSA:3.40.50.10380 - 1 101 1.5E-51
13 g3335.t29 Gene3D G3DSA:3.40.50.720 - 102 403 1.1E-118
3 g3335.t29 PANTHER PTHR23406 MALIC ENZYME-RELATED 1 388 5.7E-183
4 g3335.t29 PANTHER PTHR23406:SF80 GH17657P-RELATED 1 388 5.7E-183
14 g3335.t29 PIRSF PIRSF000106 ME 1 390 7.0E-156
6 g3335.t29 PRINTS PR00072 Malic enzyme signature 15 37 1.2E-49
8 g3335.t29 PRINTS PR00072 Malic enzyme signature 75 93 1.2E-49
9 g3335.t29 PRINTS PR00072 Malic enzyme signature 100 116 1.2E-49
5 g3335.t29 PRINTS PR00072 Malic enzyme signature 131 147 1.2E-49
7 g3335.t29 PRINTS PR00072 Malic enzyme signature 234 250 1.2E-49
1 g3335.t29 Pfam PF00390 Malic enzyme, N-terminal domain 1 94 9.8E-40
2 g3335.t29 Pfam PF03949 Malic enzyme, NAD binding domain 104 357 1.1E-96
16 g3335.t29 ProSitePatterns PS00331 Malic enzymes signature. 100 116 -
17 g3335.t29 SMART SM01274 malic_2 1 94 3.3E-22
18 g3335.t29 SMART SM00919 Malic_M_2 104 357 1.8E-110
11 g3335.t29 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 103 2.3E-45
10 g3335.t29 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 104 398 3.1E-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

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