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.t6 TSS g12344.t6 22650458 22650458
chr_1 g12344 g12344.t6 isoform g12344.t6 22650606 22652413
chr_1 g12344 g12344.t6 exon g12344.t6.exon1 22650606 22650644
chr_1 g12344 g12344.t6 exon g12344.t6.exon2 22651354 22651520
chr_1 g12344 g12344.t6 cds g12344.t6.CDS1 22651428 22651520
chr_1 g12344 g12344.t6 exon g12344.t6.exon3 22651603 22652260
chr_1 g12344 g12344.t6 cds g12344.t6.CDS2 22651603 22652260
chr_1 g12344 g12344.t6 exon g12344.t6.exon4 22652316 22652413
chr_1 g12344 g12344.t6 cds g12344.t6.CDS3 22652316 22652413
chr_1 g12344 g12344.t6 TTS g12344.t6 22652547 22652547

Sequences

>g12344.t6 Gene=g12344 Length=962
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGGTAAAAGCTAAAATAATTGATGGAA
AGAAGATTTCTGAAGAAATTAAGATTGAATTACGCGAACAGATTAAAGAATGGATGCAAC
AAGAAAATGTAAGAGCTCCTCAATTGACATGCATTTTGGTTGGCGAAGATTCAGCTTCAC
AAGTCTATGTGAAGAATAAAATGAAAGCCGCAAATGATGTCGGAATAAAGAGTGAAACAA
TAAATTTACCAAAAACAATAAGTGAAGATGAACTTATTCAAATAATTGAGAGACTCAATG
ATGACAATTCAGTTGATGGAATTTTAGTTCAACTTCCATTGCCTGATCATATTGATGATA
AAAAGATTTGCAATATTGTGAGTTGTGAGAAAGATGTTGATGGATTTAATAGTACTAATC
TTGGACGTTTGAGTCAAGACTTGAATACTATGGTACCTTGTACACCACTCGGTGTTCAAG
AGCTTTTAAAAAAATATGATATCGAAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAA
GTGCACATGTTGGAAAGCCAATTCAATCTCTATTGCAATCTGATGGTCGTCATGAAATTT
CAGGAATGGATTGCACAACTATAATGTGTCACAGATTCACACCTCCAGAGAAACTTAAAA
AATTTTGCAGAGAAGCTGATATTATCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTG
AAGATATGATTAAGCCAGGTGCTTGTGTTATTGATGTCGGTATTACAAGAATCTATGATG
AAGAGACTAAAAAATCAAAGCTTGTTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTG
CTGGTTTAATTACACCTGTTCCAGGTGGAGTTGGTCCAATGACAGTTTGCATGCTGATGA
AGAACACATTTACAGCAGCAAAGAGACTTGCAAAATTACGCAAAGAGAAGCTAATTAAAT
AA

>g12344.t6 Gene=g12344 Length=282
MQQENVRAPQLTCILVGEDSASQVYVKNKMKAANDVGIKSETINLPKTISEDELIQIIER
LNDDNSVDGILVQLPLPDHIDDKKICNIVSCEKDVDGFNSTNLGRLSQDLNTMVPCTPLG
VQELLKKYDIETFGKTAVVVGRSAHVGKPIQSLLQSDGRHEISGMDCTTIMCHRFTPPEK
LKKFCREADIIIVAVGKPNLIREDMIKPGACVIDVGITRIYDEETKKSKLVGDVDFENVK
KVAGLITPVPGGVGPMTVCMLMKNTFTAAKRLAKLRKEKLIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t6 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 92 270 1.38358E-83
16 g12344.t6 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 5 266 1.6E-101
15 g12344.t6 Gene3D G3DSA:3.40.50.720 - 115 249 1.6E-101
5 g12344.t6 Hamap MF_01576 Bifunctional protein FolD [folD]. 1 273 32.373959
3 g12344.t6 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 4 278 2.6E-123
4 g12344.t6 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 4 278 2.6E-123
12 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 9 31 5.1E-80
6 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 50 77 5.1E-80
8 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 85 106 5.1E-80
11 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 130 150 5.1E-80
9 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 189 218 5.1E-80
7 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 229 245 5.1E-80
10 g12344.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 246 264 5.1E-80
2 g12344.t6 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 6 96 1.6E-34
1 g12344.t6 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 100 271 5.4E-66
18 g12344.t6 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 51 76 -
19 g12344.t6 ProSitePatterns PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. 250 258 -
14 g12344.t6 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 6 97 3.55E-33
13 g12344.t6 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 98 270 7.51E-46

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. There were no conditions that were differentially expressed