General information for g3335.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as NADP-dependent malic enzyme.
Parent gene
- The parent gene g3335 is located on chr_3: 24726455..24730040 (+ strand)
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.t1 | TSS | g3335.t1 | 24723961 | 24723961 |
| chr_3 | g3335 | g3335.t1 | isoform | g3335.t1 | 24724136 | 24727783 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon1 | 24724136 | 24724155 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS1 | 24724136 | 24724155 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon2 | 24725121 | 24725263 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS2 | 24725121 | 24725263 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon3 | 24725319 | 24725466 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS3 | 24725319 | 24725466 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon4 | 24725537 | 24725582 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS4 | 24725537 | 24725582 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon5 | 24726089 | 24726166 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS5 | 24726089 | 24726166 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon6 | 24726241 | 24726265 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS6 | 24726241 | 24726265 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon7 | 24726323 | 24727558 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS7 | 24726323 | 24727558 |
| chr_3 | g3335 | g3335.t1 | exon | g3335.t1.exon8 | 24727617 | 24727783 |
| chr_3 | g3335 | g3335.t1 | cds | g3335.t1.CDS8 | 24727617 | 24727783 |
| chr_3 | g3335 | g3335.t1 | TTS | g3335.t1 | 24727926 | 24727926 |
Sequences
>g3335.t1 Gene=g3335 Length=1863
ATGTCTCTTAGACTTTTAATTCGTAATGGGTCGTTTGCGCGATCATATCCAAATCTTGCA
ATATGTGGTACGACTTCTTCACCGAAAAAGTCAACACCCAATCAGCAAATTCGCTTGCAT
CATGAAGTTACAGGCGACATAATTGTTCCGTCTATGGTTATGGGAATTGATCATTTAAGA
GATCCGCGTTTAAATAAAGGTCTTGCATTTTCACTTCAAGAACGTCAGGTATTAGGCATT
CATGGTCTTCAACCAGCACGAATAAAGACTCAAGAAGAACAATTAGAGCTGTGTAAAATT
TCAATTATGAGATATCAAGAAGATTTAAATAAATATCAATATCTTGTAGACTTACAGGAT
CGAAATGAACGTCTATTTTTTCGTTTAGTATCAGAGAATGTTGAAATGATGATGCCCATC
ATTTATACACCAACTGTTGGTTCAGCTTGCCAAAAATTCGGCTTAATTTATCGAAGACCA
AGAGGTCTTTTCGTAACATTCAATGACAAAGGACACGTGTTTGATGTATTAAAGAACTGG
CCAGAGCCAGATGTAAGAGCTATCGTTGTTACCGATGGTGAACGTATTTTAGGTTTAGGC
GATTTAGGAGCTCAAGGAATGGGCATTCCCGTAGGAAAACTGGCACTCTACACTGCCCTT
GCTGGTATCAAACCTCATCAGTGTTTGCCGATTGTCATCGATGTGGGAACAAATAATAAA
GATCTTCTCGAAGATCCACTTTACGTTGGTTTAAGACAACCTAGAGTATCAGGACAAGCC
TATGACGATTTTATTGATGAATTCATGGAAGCAGTTGTTAAACGTTATGGACAAAATACT
TTGATTCAATTTGAAGATTTTGGAAATCACAATGCTTTCAGGTTTTTAGACAAATACCGT
GACACTTATTGCACTTTTAATGATGATATTCAAGGCACAGCATCAGTTGCTGTTGCAGGA
CTTCTTGCTTCAAAGCGTGTAACAGGAAAGAAATTGTCAGATAACAAAATTCTTTTCCTC
GGTGCTGGTGAAGCTGCTATCGGAATTGCCGATTTGTGTGTTAAGGCAATGATGACAGAA
GGAGTTTCACAAGATGAAGCGCGCGACAAGATTTGGATGGTTGATATTGATGGACTTTTA
GCAAAAGGACGACCAGAAGGGCAGTTAGGTGGTCACAAATGGTTTTATGCTAAAGAGCAT
GAAGTTATGAAAGATTTTACTGAAATTGTAAAAGAAGTAAGGCCATCAATTTTAATTGGT
GCAAGTGCTGTTGGTGGTGCTTTTACACCTGAAATTTTGCAAATGATGGCAGAATTCAAT
GAACGACCTATTATTTTTGCATTATCAAATCCAACAATTAAAGCTGAATATACTACAGAA
GCAGCTTATACACATACAAAAGGAAAATGCATTTTTGCTTCAGGTTCACCATTTGGTCAA
GTGAACTATAATGGACAAATTTTTAATCCTGGACAAGGAAATAATGCCTACATTTTTCCT
GGGGTCGCTTTAGGCGTTATTGCTACAGGCACTCATCATATTCCTGAAGACATGTTTTTA
ATTGCAGCTGAAACAATTGCAAAACACGTATCAGATGAAGATATACAAAGAGGCTCACTA
TATCCACCACTTTCAGTCATTAAAGAATGCTCATTTGATATTGCTATTGGAATTACTAAA
TACGCTTATGCCAAAGGTTTAGCAAGTTTGTATCCTGAGCCATCAGATAAGAAAACTTGG
TTGAAACAGCAACTTTATAATTTCAACTATGAAAGTTCAATGCCAATCACATGGCCTTGG
CCAGAAATGCCACACATTACCACCCGCCCTTTAGAACCTACTTTGCTTCATAAGAAAAAT
TAA
>g3335.t1 Gene=g3335 Length=620
MSLRLLIRNGSFARSYPNLAICGTTSSPKKSTPNQQIRLHHEVTGDIIVPSMVMGIDHLR
DPRLNKGLAFSLQERQVLGIHGLQPARIKTQEEQLELCKISIMRYQEDLNKYQYLVDLQD
RNERLFFRLVSENVEMMMPIIYTPTVGSACQKFGLIYRRPRGLFVTFNDKGHVFDVLKNW
PEPDVRAIVVTDGERILGLGDLGAQGMGIPVGKLALYTALAGIKPHQCLPIVIDVGTNNK
DLLEDPLYVGLRQPRVSGQAYDDFIDEFMEAVVKRYGQNTLIQFEDFGNHNAFRFLDKYR
DTYCTFNDDIQGTASVAVAGLLASKRVTGKKLSDNKILFLGAGEAAIGIADLCVKAMMTE
GVSQDEARDKIWMVDIDGLLAKGRPEGQLGGHKWFYAKEHEVMKDFTEIVKEVRPSILIG
ASAVGGAFTPEILQMMAEFNERPIIFALSNPTIKAEYTTEAAYTHTKGKCIFASGSPFGQ
VNYNGQIFNPGQGNNAYIFPGVALGVIATGTHHIPEDMFLIAAETIAKHVSDEDIQRGSL
YPPLSVIKECSFDIAIGITKYAYAKGLASLYPEPSDKKTWLKQQLYNFNYESSMPITWPW
PEMPHITTRPLEPTLLHKKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g3335.t1 | CDD | cd05312 | NAD_bind_1_malic_enz | 310 | 587 | 1.07727E-144 |
| 18 | g3335.t1 | Coils | Coil | Coil | 88 | 108 | - |
| 16 | g3335.t1 | Gene3D | G3DSA:3.30.2330.30 | - | 37 | 602 | 2.7E-271 |
| 17 | g3335.t1 | Gene3D | G3DSA:1.20.1370.30 | - | 52 | 160 | 2.7E-271 |
| 14 | g3335.t1 | Gene3D | G3DSA:3.40.50.10380 | - | 161 | 566 | 2.7E-271 |
| 15 | g3335.t1 | Gene3D | G3DSA:3.40.50.720 | - | 308 | 494 | 2.7E-271 |
| 3 | g3335.t1 | PANTHER | PTHR23406 | MALIC ENZYME-RELATED | 45 | 594 | 2.1E-260 |
| 4 | g3335.t1 | PANTHER | PTHR23406:SF80 | GH17657P-RELATED | 45 | 594 | 2.1E-260 |
| 19 | g3335.t1 | PIRSF | PIRSF000106 | ME | 26 | 596 | 7.5E-219 |
| 8 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 125 | 149 | 2.3E-78 |
| 6 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 185 | 214 | 2.3E-78 |
| 5 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 221 | 243 | 2.3E-78 |
| 10 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 281 | 299 | 2.3E-78 |
| 7 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 306 | 322 | 2.3E-78 |
| 11 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 337 | 353 | 2.3E-78 |
| 9 | g3335.t1 | PRINTS | PR00072 | Malic enzyme signature | 440 | 456 | 2.3E-78 |
| 1 | g3335.t1 | Pfam | PF00390 | Malic enzyme, N-terminal domain | 119 | 300 | 3.3E-80 |
| 2 | g3335.t1 | Pfam | PF03949 | Malic enzyme, NAD binding domain | 310 | 563 | 3.1E-96 |
| 23 | g3335.t1 | ProSitePatterns | PS00331 | Malic enzymes signature. | 306 | 322 | - |
| 21 | g3335.t1 | SMART | SM01274 | malic_2 | 119 | 300 | 4.8E-109 |
| 22 | g3335.t1 | SMART | SM00919 | Malic_M_2 | 310 | 563 | 1.8E-110 |
| 13 | g3335.t1 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 39 | 309 | 8.63E-108 |
| 12 | g3335.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 310 | 604 | 1.34E-96 |
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 transcript has been annotated with K00029 (malate dehydrogenase (oxaloacetate-decarboxylating)(NADP+))
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.
