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.t1 TSS g12344.t1 22650458 22650458
chr_1 g12344 g12344.t1 isoform g12344.t1 22650606 22652413
chr_1 g12344 g12344.t1 exon g12344.t1.exon1 22650606 22650640
chr_1 g12344 g12344.t1 cds g12344.t1.CDS1 22650606 22650640
chr_1 g12344 g12344.t1 exon g12344.t1.exon2 22651340 22651520
chr_1 g12344 g12344.t1 cds g12344.t1.CDS2 22651340 22651520
chr_1 g12344 g12344.t1 exon g12344.t1.exon3 22651603 22652260
chr_1 g12344 g12344.t1 cds g12344.t1.CDS3 22651603 22652260
chr_1 g12344 g12344.t1 exon g12344.t1.exon4 22652316 22652413
chr_1 g12344 g12344.t1 cds g12344.t1.CDS4 22652316 22652413
chr_1 g12344 g12344.t1 TTS g12344.t1 22652547 22652547

Sequences

>g12344.t1 Gene=g12344 Length=972
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGTCCAGAGCCAATAGAAGCTAAAATA
ATTGATGGAAAGAAGATTTCTGAAGAAATTAAGATTGAATTACGCGAACAGATTAAAGAA
TGGATGCAACAAGAAAATGTAAGAGCTCCTCAATTGACATGCATTTTGGTTGGCGAAGAT
TCAGCTTCACAAGTCTATGTGAAGAATAAAATGAAAGCCGCAAATGATGTCGGAATAAAG
AGTGAAACAATAAATTTACCAAAAACAATAAGTGAAGATGAACTTATTCAAATAATTGAG
AGACTCAATGATGACAATTCAGTTGATGGAATTTTAGTTCAACTTCCATTGCCTGATCAT
ATTGATGATAAAAAGATTTGCAATATTGTGAGTTGTGAGAAAGATGTTGATGGATTTAAT
AGTACTAATCTTGGACGTTTGAGTCAAGACTTGAATACTATGGTACCTTGTACACCACTC
GGTGTTCAAGAGCTTTTAAAAAAATATGATATCGAAACATTCGGCAAAACTGCTGTCGTT
GTTGGAAGAAGTGCACATGTTGGAAAGCCAATTCAATCTCTATTGCAATCTGATGGTCGT
CATGAAATTTCAGGAATGGATTGCACAACTATAATGTGTCACAGATTCACACCTCCAGAG
AAACTTAAAAAATTTTGCAGAGAAGCTGATATTATCATTGTTGCCGTTGGAAAACCAAAT
TTAATTCGTGAAGATATGATTAAGCCAGGTGCTTGTGTTATTGATGTCGGTATTACAAGA
ATCTATGATGAAGAGACTAAAAAATCAAAGCTTGTTGGTGATGTTGATTTTGAAAATGTA
AAGAAAGTTGCTGGTTTAATTACACCTGTTCCAGGTGGAGTTGGTCCAATGACAGTTTGC
ATGCTGATGAAGAACACATTTACAGCAGCAAAGAGACTTGCAAAATTACGCAAAGAGAAG
CTAATTAAATAA

>g12344.t1 Gene=g12344 Length=323
MAPNPHSEVPLRPEPIEAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGED
SASQVYVKNKMKAANDVGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDH
IDDKKICNIVSCEKDVDGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVV
VGRSAHVGKPIQSLLQSDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPN
LIREDMIKPGACVIDVGITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGGVGPMTVC
MLMKNTFTAAKRLAKLRKEKLIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t1 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 133 311 1.31127E-83
15 g12344.t1 Gene3D G3DSA:3.40.50.720 - 21 290 1.1E-107
16 g12344.t1 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 23 307 1.1E-107
5 g12344.t1 Hamap MF_01576 Bifunctional protein FolD [folD]. 18 314 36.726048
3 g12344.t1 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 18 319 1.8E-132
4 g12344.t1 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 18 319 1.8E-132
7 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 50 72 8.9E-80
8 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 91 118 8.9E-80
9 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 126 147 8.9E-80
11 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 171 191 8.9E-80
10 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 230 259 8.9E-80
6 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 270 286 8.9E-80
12 g12344.t1 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 287 305 8.9E-80
2 g12344.t1 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 20 137 3.2E-40
1 g12344.t1 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 141 312 7.8E-66
18 g12344.t1 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 92 117 -
19 g12344.t1 ProSitePatterns PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. 291 299 -
14 g12344.t1 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 18 138 2.4E-40
13 g12344.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 139 311 1.06E-45

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

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