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.t11 TSS g12344.t11 22650458 22650458
chr_1 g12344 g12344.t11 isoform g12344.t11 22650606 22652413
chr_1 g12344 g12344.t11 exon g12344.t11.exon1 22650606 22650846
chr_1 g12344 g12344.t11 cds g12344.t11.CDS1 22650839 22650846
chr_1 g12344 g12344.t11 exon g12344.t11.exon2 22651340 22651520
chr_1 g12344 g12344.t11 cds g12344.t11.CDS2 22651340 22651520
chr_1 g12344 g12344.t11 exon g12344.t11.exon3 22651603 22652413
chr_1 g12344 g12344.t11 cds g12344.t11.CDS3 22651603 22652268
chr_1 g12344 g12344.t11 TTS g12344.t11 22652547 22652547

Sequences

>g12344.t11 Gene=g12344 Length=1233
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGGTAAGTAGAGAAAAGAAGAAAGCAT
TTTGTTGCTAGGGAAAATGTGTTTTGCATTTCATCATTTCAAATTAGTATTTCTGTGACA
ATTAAACGATACACACTCTTTTATTTTATTTTATCCATCGTATAAACATTTTCTCTGTAT
AATTTAGTATTCGGACTAAGCTAAAGATGTCGTATAGTTCTTCATTATCTTCTATGCCAA
TTCCAGAGCCAATAGAAGCTAAAATAATTGATGGAAAGAAGATTTCTGAAGAAATTAAGA
TTGAATTACGCGAACAGATTAAAGAATGGATGCAACAAGAAAATGTAAGAGCTCCTCAAT
TGACATGCATTTTGGTTGGCGAAGATTCAGCTTCACAAGTCTATGTGAAGAATAAAATGA
AAGCCGCAAATGATGTCGGAATAAAGAGTGAAACAATAAATTTACCAAAAACAATAAGTG
AAGATGAACTTATTCAAATAATTGAGAGACTCAATGATGACAATTCAGTTGATGGAATTT
TAGTTCAACTTCCATTGCCTGATCATATTGATGATAAAAAGATTTGCAATATTGTGAGTT
GTGAGAAAGATGTTGATGGATTTAATAGTACTAATCTTGGACGTTTGAGTCAAGACTTGA
ATACTATGGTACCTTGTACACCACTCGGTGTTCAAGAGCTTTTAAAAAAATATGATATCG
AAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAAGTGCACATGTTGGAAAGCCAATTC
AATCTCTATTGCAATCTGATGGTCGTCATGAAATTTCAGGAATGGATTGCACAACTATAA
TGTGTCACAGATTCACACCTCCAGAGAAACTTAAAAAATTTTGCAGAGAAGCTGATATTA
TCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTGAAGATATGATTAAGCCAGGTGCTT
GTGTTATTGATGTCGGTATTACAAGAATCTATGATGAAGAGACTAAAAAATCAAAGCTTG
TTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTGCTGGTTTAATTACACCTGTTCCAG
GTTTGTAACTTTATCATTTGATTAATGCACATTTCTAATTTGTCAAATTTTTTAGGTGGA
GTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAGCAGCAAAGAGACTT
GCAAAATTACGCAAAGAGAAGCTAATTAAATAA

>g12344.t11 Gene=g12344 Length=284
MPIPEPIEAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGEDSASQVYVKN
KMKAANDVGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDHIDDKKICNI
VSCEKDVDGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVVVGRSAHVGK
PIQSLLQSDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPNLIREDMIKP
GACVIDVGITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t11 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 124 283 4.39876E-69
15 g12344.t11 Gene3D G3DSA:3.40.50.720 - 12 281 2.1E-96
16 g12344.t11 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 14 283 2.1E-96
5 g12344.t11 Hamap MF_01576 Bifunctional protein FolD [folD]. 9 284 30.371271
3 g12344.t11 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 9 283 3.4E-117
4 g12344.t11 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 9 283 3.4E-117
10 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 41 63 1.3E-69
12 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 82 109 1.3E-69
9 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 117 138 1.3E-69
6 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 162 182 1.3E-69
8 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 221 250 1.3E-69
11 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 261 277 1.3E-69
7 g12344.t11 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 278 284 1.3E-69
2 g12344.t11 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 11 128 2.4E-40
1 g12344.t11 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 132 283 1.4E-53
18 g12344.t11 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 83 108 -
14 g12344.t11 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 9 129 1.82E-40
13 g12344.t11 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 130 283 4.96E-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. There were no conditions that were differentially expressed