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.t18 TSS g12344.t18 22650458 22650458
chr_1 g12344 g12344.t18 isoform g12344.t18 22651339 22652413
chr_1 g12344 g12344.t18 exon g12344.t18.exon1 22651339 22651520
chr_1 g12344 g12344.t18 cds g12344.t18.CDS1 22651428 22651520
chr_1 g12344 g12344.t18 exon g12344.t18.exon2 22651603 22652413
chr_1 g12344 g12344.t18 cds g12344.t18.CDS2 22651603 22652268
chr_1 g12344 g12344.t18 TTS g12344.t18 22652547 22652547

Sequences

>g12344.t18 Gene=g12344 Length=993
GTCCAGAGCCAATAGAAGCTAAAATAATTGATGGAAAGAAGATTTCTGAAGAAATTAAGA
TTGAATTACGCGAACAGATTAAAGAATGGATGCAACAAGAAAATGTAAGAGCTCCTCAAT
TGACATGCATTTTGGTTGGCGAAGATTCAGCTTCACAAGTCTATGTGAAGAATAAAATGA
AAGCCGCAAATGATGTCGGAATAAAGAGTGAAACAATAAATTTACCAAAAACAATAAGTG
AAGATGAACTTATTCAAATAATTGAGAGACTCAATGATGACAATTCAGTTGATGGAATTT
TAGTTCAACTTCCATTGCCTGATCATATTGATGATAAAAAGATTTGCAATATTGTGAGTT
GTGAGAAAGATGTTGATGGATTTAATAGTACTAATCTTGGACGTTTGAGTCAAGACTTGA
ATACTATGGTACCTTGTACACCACTCGGTGTTCAAGAGCTTTTAAAAAAATATGATATCG
AAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAAGTGCACATGTTGGAAAGCCAATTC
AATCTCTATTGCAATCTGATGGTCGTCATGAAATTTCAGGAATGGATTGCACAACTATAA
TGTGTCACAGATTCACACCTCCAGAGAAACTTAAAAAATTTTGCAGAGAAGCTGATATTA
TCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTGAAGATATGATTAAGCCAGGTGCTT
GTGTTATTGATGTCGGTATTACAAGAATCTATGATGAAGAGACTAAAAAATCAAAGCTTG
TTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTGCTGGTTTAATTACACCTGTTCCAG
GTTTGTAACTTTATCATTTGATTAATGCACATTTCTAATTTGTCAAATTTTTTAGGTGGA
GTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAGCAGCAAAGAGACTT
GCAAAATTACGCAAAGAGAAGCTAATTAAATAA

>g12344.t18 Gene=g12344 Length=252
MQQENVRAPQLTCILVGEDSASQVYVKNKMKAANDVGIKSETINLPKTISEDELIQIIER
LNDDNSVDGILVQLPLPDHIDDKKICNIVSCEKDVDGFNSTNLGRLSQDLNTMVPCTPLG
VQELLKKYDIETFGKTAVVVGRSAHVGKPIQSLLQSDGRHEISGMDCTTIMCHRFTPPEK
LKKFCREADIIIVAVGKPNLIREDMIKPGACVIDVGITRIYDEETKKSKLVGDVDFENVK
KVAGLITPVPGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t18 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 92 251 3.55102E-69
16 g12344.t18 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 5 251 2.3E-90
15 g12344.t18 Gene3D G3DSA:3.40.50.720 - 115 249 2.3E-90
5 g12344.t18 Hamap MF_01576 Bifunctional protein FolD [folD]. 1 252 26.01918
3 g12344.t18 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 4 251 4.5E-108
4 g12344.t18 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 4 251 4.5E-108
12 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 9 31 5.5E-70
6 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 50 77 5.5E-70
8 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 85 106 5.5E-70
11 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 130 150 5.5E-70
10 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 189 218 5.5E-70
7 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 229 245 5.5E-70
9 g12344.t18 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 246 252 5.5E-70
2 g12344.t18 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 6 96 1.2E-34
1 g12344.t18 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 100 251 1.0E-53
18 g12344.t18 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 51 76 -
14 g12344.t18 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 6 97 2.78E-33
13 g12344.t18 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 98 251 3.27E-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