Gene loci information

Transcript annotation

  • This transcript has been annotated as Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial.

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_1 g12344 g12344.t3 TSS g12344.t3 22650458 22650458
chr_1 g12344 g12344.t3 isoform g12344.t3 22650606 22652413
chr_1 g12344 g12344.t3 exon g12344.t3.exon1 22650606 22650640
chr_1 g12344 g12344.t3 cds g12344.t3.CDS1 22650606 22650640
chr_1 g12344 g12344.t3 exon g12344.t3.exon2 22651340 22651520
chr_1 g12344 g12344.t3 cds g12344.t3.CDS2 22651340 22651520
chr_1 g12344 g12344.t3 exon g12344.t3.exon3 22651603 22652413
chr_1 g12344 g12344.t3 cds g12344.t3.CDS3 22651603 22652268
chr_1 g12344 g12344.t3 TTS g12344.t3 22652547 22652547

Sequences

>g12344.t3 Gene=g12344 Length=1027
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGTCCAGAGCCAATAGAAGCTAAAATA
ATTGATGGAAAGAAGATTTCTGAAGAAATTAAGATTGAATTACGCGAACAGATTAAAGAA
TGGATGCAACAAGAAAATGTAAGAGCTCCTCAATTGACATGCATTTTGGTTGGCGAAGAT
TCAGCTTCACAAGTCTATGTGAAGAATAAAATGAAAGCCGCAAATGATGTCGGAATAAAG
AGTGAAACAATAAATTTACCAAAAACAATAAGTGAAGATGAACTTATTCAAATAATTGAG
AGACTCAATGATGACAATTCAGTTGATGGAATTTTAGTTCAACTTCCATTGCCTGATCAT
ATTGATGATAAAAAGATTTGCAATATTGTGAGTTGTGAGAAAGATGTTGATGGATTTAAT
AGTACTAATCTTGGACGTTTGAGTCAAGACTTGAATACTATGGTACCTTGTACACCACTC
GGTGTTCAAGAGCTTTTAAAAAAATATGATATCGAAACATTCGGCAAAACTGCTGTCGTT
GTTGGAAGAAGTGCACATGTTGGAAAGCCAATTCAATCTCTATTGCAATCTGATGGTCGT
CATGAAATTTCAGGAATGGATTGCACAACTATAATGTGTCACAGATTCACACCTCCAGAG
AAACTTAAAAAATTTTGCAGAGAAGCTGATATTATCATTGTTGCCGTTGGAAAACCAAAT
TTAATTCGTGAAGATATGATTAAGCCAGGTGCTTGTGTTATTGATGTCGGTATTACAAGA
ATCTATGATGAAGAGACTAAAAAATCAAAGCTTGTTGGTGATGTTGATTTTGAAAATGTA
AAGAAAGTTGCTGGTTTAATTACACCTGTTCCAGGTTTGTAACTTTATCATTTGATTAAT
GCACATTTCTAATTTGTCAAATTTTTTAGGTGGAGTTGGTCCAATGACAGTTTGCATGCT
GATGAAGAACACATTTACAGCAGCAAAGAGACTTGCAAAATTACGCAAAGAGAAGCTAAT
TAAATAA

>g12344.t3 Gene=g12344 Length=293
MAPNPHSEVPLRPEPIEAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGED
SASQVYVKNKMKAANDVGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDH
IDDKKICNIVSCEKDVDGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVV
VGRSAHVGKPIQSLLQSDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPN
LIREDMIKPGACVIDVGITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t3 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 133 292 3.56231E-69
15 g12344.t3 Gene3D G3DSA:3.40.50.720 - 21 290 2.4E-96
16 g12344.t3 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 23 292 2.4E-96
5 g12344.t3 Hamap MF_01576 Bifunctional protein FolD [folD]. 18 293 30.371271
3 g12344.t3 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 18 292 3.8E-117
4 g12344.t3 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 18 292 3.8E-117
7 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 50 72 1.5E-69
9 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 91 118 1.5E-69
10 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 126 147 1.5E-69
12 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 171 191 1.5E-69
11 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 230 259 1.5E-69
6 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 270 286 1.5E-69
8 g12344.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 287 293 1.5E-69
2 g12344.t3 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 20 137 2.6E-40
1 g12344.t3 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 141 292 1.5E-53
18 g12344.t3 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 92 117 -
14 g12344.t3 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 18 138 1.92E-40
13 g12344.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 139 292 5.46E-38

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:0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity MF
GO:0003824 catalytic activity 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