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.t11 TSS g3335.t11 24723961 24723961
chr_3 g3335 g3335.t11 isoform g3335.t11 24724136 24727783
chr_3 g3335 g3335.t11 exon g3335.t11.exon1 24724136 24724163
chr_3 g3335 g3335.t11 exon g3335.t11.exon2 24725121 24725263
chr_3 g3335 g3335.t11 cds g3335.t11.CDS1 24725254 24725263
chr_3 g3335 g3335.t11 exon g3335.t11.exon3 24725319 24725466
chr_3 g3335 g3335.t11 cds g3335.t11.CDS2 24725319 24725466
chr_3 g3335 g3335.t11 exon g3335.t11.exon4 24725537 24725582
chr_3 g3335 g3335.t11 cds g3335.t11.CDS3 24725537 24725582
chr_3 g3335 g3335.t11 exon g3335.t11.exon5 24726089 24726166
chr_3 g3335 g3335.t11 cds g3335.t11.CDS4 24726089 24726166
chr_3 g3335 g3335.t11 exon g3335.t11.exon6 24726241 24726265
chr_3 g3335 g3335.t11 cds g3335.t11.CDS5 24726241 24726265
chr_3 g3335 g3335.t11 exon g3335.t11.exon7 24726323 24727558
chr_3 g3335 g3335.t11 cds g3335.t11.CDS6 24726323 24727558
chr_3 g3335 g3335.t11 exon g3335.t11.exon8 24727617 24727783
chr_3 g3335 g3335.t11 cds g3335.t11.CDS7 24727617 24727783
chr_3 g3335 g3335.t11 TTS g3335.t11 24727926 24727926

Sequences

>g3335.t11 Gene=g3335 Length=1871
ATGTCTCTTAGACTTTTAATGTAAGTGCTCGTAATGGGTCGTTTGCGCGATCATATCCAA
ATCTTGCAATATGTGGTACGACTTCTTCACCGAAAAAGTCAACACCCAATCAGCAAATTC
GCTTGCATCATGAAGTTACAGGCGACATAATTGTTCCGTCTATGGTTATGGGAATTGATC
ATTTAAGAGATCCGCGTTTAAATAAAGGTCTTGCATTTTCACTTCAAGAACGTCAGGTAT
TAGGCATTCATGGTCTTCAACCAGCACGAATAAAGACTCAAGAAGAACAATTAGAGCTGT
GTAAAATTTCAATTATGAGATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGACT
TACAGGATCGAAATGAACGTCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGATGA
TGCCCATCATTTATACACCAACTGTTGGTTCAGCTTGCCAAAAATTCGGCTTAATTTATC
GAAGACCAAGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAA
AGAACTGGCCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAG
GTTTAGGCGATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACA
CTGCCCTTGCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAA
ATAATAAAGATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAG
GACAAGCCTATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGAC
AAAATACTTTGATTCAATTTGAAGATTTTGGAAATCACAATGCTTTCAGGTTTTTAGACA
AATACCGTGACACTTATTGCACTTTTAATGATGATATTCAAGGCACAGCATCAGTTGCTG
TTGCAGGACTTCTTGCTTCAAAGCGTGTAACAGGAAAGAAATTGTCAGATAACAAAATTC
TTTTCCTCGGTGCTGGTGAAGCTGCTATCGGAATTGCCGATTTGTGTGTTAAGGCAATGA
TGACAGAAGGAGTTTCACAAGATGAAGCGCGCGACAAGATTTGGATGGTTGATATTGATG
GACTTTTAGCAAAAGGACGACCAGAAGGGCAGTTAGGTGGTCACAAATGGTTTTATGCTA
AAGAGCATGAAGTTATGAAAGATTTTACTGAAATTGTAAAAGAAGTAAGGCCATCAATTT
TAATTGGTGCAAGTGCTGTTGGTGGTGCTTTTACACCTGAAATTTTGCAAATGATGGCAG
AATTCAATGAACGACCTATTATTTTTGCATTATCAAATCCAACAATTAAAGCTGAATATA
CTACAGAAGCAGCTTATACACATACAAAAGGAAAATGCATTTTTGCTTCAGGTTCACCAT
TTGGTCAAGTGAACTATAATGGACAAATTTTTAATCCTGGACAAGGAAATAATGCCTACA
TTTTTCCTGGGGTCGCTTTAGGCGTTATTGCTACAGGCACTCATCATATTCCTGAAGACA
TGTTTTTAATTGCAGCTGAAACAATTGCAAAACACGTATCAGATGAAGATATACAAAGAG
GCTCACTATATCCACCACTTTCAGTCATTAAAGAATGCTCATTTGATATTGCTATTGGAA
TTACTAAATACGCTTATGCCAAAGGTTTAGCAAGTTTGTATCCTGAGCCATCAGATAAGA
AAACTTGGTTGAAACAGCAACTTTATAATTTCAACTATGAAAGTTCAATGCCAATCACAT
GGCCTTGGCCAGAAATGCCACACATTACCACCCGCCCTTTAGAACCTACTTTGCTTCATA
AGAAAAATTAA

>g3335.t11 Gene=g3335 Length=569
MVMGIDHLRDPRLNKGLAFSLQERQVLGIHGLQPARIKTQEEQLELCKISIMRYQEDLNK
YQYLVDLQDRNERLFFRLVSENVEMMMPIIYTPTVGSACQKFGLIYRRPRGLFVTFNDKG
HVFDVLKNWPEPDVRAIVVTDGERILGLGDLGAQGMGIPVGKLALYTALAGIKPHQCLPI
VIDVGTNNKDLLEDPLYVGLRQPRVSGQAYDDFIDEFMEAVVKRYGQNTLIQFEDFGNHN
AFRFLDKYRDTYCTFNDDIQGTASVAVAGLLASKRVTGKKLSDNKILFLGAGEAAIGIAD
LCVKAMMTEGVSQDEARDKIWMVDIDGLLAKGRPEGQLGGHKWFYAKEHEVMKDFTEIVK
EVRPSILIGASAVGGAFTPEILQMMAEFNERPIIFALSNPTIKAEYTTEAAYTHTKGKCI
FASGSPFGQVNYNGQIFNPGQGNNAYIFPGVALGVIATGTHHIPEDMFLIAAETIAKHVS
DEDIQRGSLYPPLSVIKECSFDIAIGITKYAYAKGLASLYPEPSDKKTWLKQQLYNFNYE
SSMPITWPWPEMPHITTRPLEPTLLHKKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g3335.t11 CDD cd05312 NAD_bind_1_malic_enz 259 536 3.26406E-145
18 g3335.t11 Coils Coil Coil 37 57 -
17 g3335.t11 Gene3D G3DSA:1.20.1370.30 - 4 109 1.3E-270
14 g3335.t11 Gene3D G3DSA:3.40.50.10380 - 110 515 1.3E-270
15 g3335.t11 Gene3D G3DSA:3.40.50.720 - 257 443 1.3E-270
16 g3335.t11 Gene3D G3DSA:3.30.2330.30 - 516 551 1.3E-270
3 g3335.t11 PANTHER PTHR23406 MALIC ENZYME-RELATED 3 543 1.5E-259
4 g3335.t11 PANTHER PTHR23406:SF80 GH17657P-RELATED 3 543 1.5E-259
19 g3335.t11 PIRSF PIRSF000106 ME 1 545 2.3E-218
5 g3335.t11 PRINTS PR00072 Malic enzyme signature 74 98 1.5E-78
7 g3335.t11 PRINTS PR00072 Malic enzyme signature 134 163 1.5E-78
11 g3335.t11 PRINTS PR00072 Malic enzyme signature 170 192 1.5E-78
9 g3335.t11 PRINTS PR00072 Malic enzyme signature 230 248 1.5E-78
10 g3335.t11 PRINTS PR00072 Malic enzyme signature 255 271 1.5E-78
8 g3335.t11 PRINTS PR00072 Malic enzyme signature 286 302 1.5E-78
6 g3335.t11 PRINTS PR00072 Malic enzyme signature 389 405 1.5E-78
1 g3335.t11 Pfam PF00390 Malic enzyme, N-terminal domain 68 249 2.8E-80
2 g3335.t11 Pfam PF03949 Malic enzyme, NAD binding domain 259 512 2.6E-96
23 g3335.t11 ProSitePatterns PS00331 Malic enzymes signature. 255 271 -
21 g3335.t11 SMART SM01274 malic_2 68 249 4.8E-109
22 g3335.t11 SMART SM00919 Malic_M_2 259 512 1.8E-110
13 g3335.t11 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 3 258 1.01E-106
12 g3335.t11 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 259 553 9.67E-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