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.t10 TSS g12344.t10 22650458 22650458
chr_1 g12344 g12344.t10 isoform g12344.t10 22650606 22652413
chr_1 g12344 g12344.t10 exon g12344.t10.exon1 22650606 22650846
chr_1 g12344 g12344.t10 cds g12344.t10.CDS1 22650839 22650846
chr_1 g12344 g12344.t10 exon g12344.t10.exon2 22651340 22651520
chr_1 g12344 g12344.t10 cds g12344.t10.CDS2 22651340 22651520
chr_1 g12344 g12344.t10 exon g12344.t10.exon3 22651603 22652260
chr_1 g12344 g12344.t10 cds g12344.t10.CDS3 22651603 22652260
chr_1 g12344 g12344.t10 exon g12344.t10.exon4 22652316 22652413
chr_1 g12344 g12344.t10 cds g12344.t10.CDS4 22652316 22652413
chr_1 g12344 g12344.t10 TTS g12344.t10 22652547 22652547

Sequences

>g12344.t10 Gene=g12344 Length=1178
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGGTAAGTAGAGAAAAGAAGAAAGCAT
TTTGTTGCTAGGGAAAATGTGTTTTGCATTTCATCATTTCAAATTAGTATTTCTGTGACA
ATTAAACGATACACACTCTTTTATTTTATTTTATCCATCGTATAAACATTTTCTCTGTAT
AATTTAGTATTCGGACTAAGCTAAAGATGTCGTATAGTTCTTCATTATCTTCTATGCCAA
TTCCAGAGCCAATAGAAGCTAAAATAATTGATGGAAAGAAGATTTCTGAAGAAATTAAGA
TTGAATTACGCGAACAGATTAAAGAATGGATGCAACAAGAAAATGTAAGAGCTCCTCAAT
TGACATGCATTTTGGTTGGCGAAGATTCAGCTTCACAAGTCTATGTGAAGAATAAAATGA
AAGCCGCAAATGATGTCGGAATAAAGAGTGAAACAATAAATTTACCAAAAACAATAAGTG
AAGATGAACTTATTCAAATAATTGAGAGACTCAATGATGACAATTCAGTTGATGGAATTT
TAGTTCAACTTCCATTGCCTGATCATATTGATGATAAAAAGATTTGCAATATTGTGAGTT
GTGAGAAAGATGTTGATGGATTTAATAGTACTAATCTTGGACGTTTGAGTCAAGACTTGA
ATACTATGGTACCTTGTACACCACTCGGTGTTCAAGAGCTTTTAAAAAAATATGATATCG
AAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAAGTGCACATGTTGGAAAGCCAATTC
AATCTCTATTGCAATCTGATGGTCGTCATGAAATTTCAGGAATGGATTGCACAACTATAA
TGTGTCACAGATTCACACCTCCAGAGAAACTTAAAAAATTTTGCAGAGAAGCTGATATTA
TCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTGAAGATATGATTAAGCCAGGTGCTT
GTGTTATTGATGTCGGTATTACAAGAATCTATGATGAAGAGACTAAAAAATCAAAGCTTG
TTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTGCTGGTTTAATTACACCTGTTCCAG
GTGGAGTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAGCAGCAAAGA
GACTTGCAAAATTACGCAAAGAGAAGCTAATTAAATAA

>g12344.t10 Gene=g12344 Length=314
MPIPEPIEAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGEDSASQVYVKN
KMKAANDVGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDHIDDKKICNI
VSCEKDVDGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVVVGRSAHVGK
PIQSLLQSDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPNLIREDMIKP
GACVIDVGITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGGVGPMTVCMLMKNTFTA
AKRLAKLRKEKLIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t10 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 124 302 1.61127E-83
15 g12344.t10 Gene3D G3DSA:3.40.50.720 - 12 281 9.9E-108
16 g12344.t10 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 14 298 9.9E-108
5 g12344.t10 Hamap MF_01576 Bifunctional protein FolD [folD]. 9 305 36.726048
3 g12344.t10 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 9 310 1.6E-132
4 g12344.t10 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 9 310 1.6E-132
10 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 41 63 7.9E-80
12 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 82 109 7.9E-80
9 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 117 138 7.9E-80
6 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 162 182 7.9E-80
8 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 221 250 7.9E-80
11 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 261 277 7.9E-80
7 g12344.t10 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 278 296 7.9E-80
2 g12344.t10 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 11 128 3.0E-40
1 g12344.t10 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 132 303 7.3E-66
18 g12344.t10 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 83 108 -
19 g12344.t10 ProSitePatterns PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. 282 290 -
14 g12344.t10 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 9 129 2.21E-40
13 g12344.t10 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 130 302 1.03E-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