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.t7 TSS g12344.t7 22650458 22650458
chr_1 g12344 g12344.t7 isoform g12344.t7 22650606 22652413
chr_1 g12344 g12344.t7 exon g12344.t7.exon1 22650606 22650624
chr_1 g12344 g12344.t7 cds g12344.t7.CDS1 22650606 22650624
chr_1 g12344 g12344.t7 exon g12344.t7.exon2 22651354 22651520
chr_1 g12344 g12344.t7 cds g12344.t7.CDS2 22651354 22651520
chr_1 g12344 g12344.t7 exon g12344.t7.exon3 22651603 22652264
chr_1 g12344 g12344.t7 cds g12344.t7.CDS3 22651603 22652264
chr_1 g12344 g12344.t7 exon g12344.t7.exon4 22652316 22652413
chr_1 g12344 g12344.t7 cds g12344.t7.CDS4 22652316 22652409
chr_1 g12344 g12344.t7 TTS g12344.t7 22652547 22652547

Sequences

>g12344.t7 Gene=g12344 Length=946
ATGGCACCAAATCCACATAAAGCTAAAATAATTGATGGAAAGAAGATTTCTGAAGAAATT
AAGATTGAATTACGCGAACAGATTAAAGAATGGATGCAACAAGAAAATGTAAGAGCTCCT
CAATTGACATGCATTTTGGTTGGCGAAGATTCAGCTTCACAAGTCTATGTGAAGAATAAA
ATGAAAGCCGCAAATGATGTCGGAATAAAGAGTGAAACAATAAATTTACCAAAAACAATA
AGTGAAGATGAACTTATTCAAATAATTGAGAGACTCAATGATGACAATTCAGTTGATGGA
ATTTTAGTTCAACTTCCATTGCCTGATCATATTGATGATAAAAAGATTTGCAATATTGTG
AGTTGTGAGAAAGATGTTGATGGATTTAATAGTACTAATCTTGGACGTTTGAGTCAAGAC
TTGAATACTATGGTACCTTGTACACCACTCGGTGTTCAAGAGCTTTTAAAAAAATATGAT
ATCGAAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAAGTGCACATGTTGGAAAGCCA
ATTCAATCTCTATTGCAATCTGATGGTCGTCATGAAATTTCAGGAATGGATTGCACAACT
ATAATGTGTCACAGATTCACACCTCCAGAGAAACTTAAAAAATTTTGCAGAGAAGCTGAT
ATTATCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTGAAGATATGATTAAGCCAGGT
GCTTGTGTTATTGATGTCGGTATTACAAGAATCTATGATGAAGAGACTAAAAAATCAAAG
CTTGTTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTGCTGGTTTAATTACACCTGTT
CCAGGTTTGTGGAGTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAGC
AGCAAAGAGACTTGCAAAATTACGCAAAGAGAAGCTAATTAAATAA

>g12344.t7 Gene=g12344 Length=313
MAPNPHKAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGEDSASQVYVKNK
MKAANDVGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDHIDDKKICNIV
SCEKDVDGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVVVGRSAHVGKP
IQSLLQSDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPNLIREDMIKPG
ACVIDVGITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGLWSWSNDSLHADEEHIYS
SKETCKITQREAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12344.t7 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 123 282 2.41208E-70
15 g12344.t7 Gene3D G3DSA:3.40.50.720 - 11 280 2.5E-96
16 g12344.t7 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 13 282 2.5E-96
5 g12344.t7 Hamap MF_01576 Bifunctional protein FolD [folD]. 8 304 32.51368
3 g12344.t7 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 7 282 1.1E-117
4 g12344.t7 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 7 282 1.1E-117
9 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 40 62 4.7E-67
11 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 81 108 4.7E-67
10 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 116 137 4.7E-67
8 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 161 181 4.7E-67
12 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 220 249 4.7E-67
7 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 260 276 4.7E-67
6 g12344.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 277 295 4.7E-67
2 g12344.t7 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 10 127 3.0E-40
1 g12344.t7 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 131 282 1.8E-53
18 g12344.t7 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 82 107 -
14 g12344.t7 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 8 128 2.4E-40
13 g12344.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 129 282 3.95E-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