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.t13 TSS g12344.t13 22650458 22650458
chr_1 g12344 g12344.t13 isoform g12344.t13 22650606 22652413
chr_1 g12344 g12344.t13 exon g12344.t13.exon1 22650606 22651271
chr_1 g12344 g12344.t13 cds g12344.t13.CDS1 22651105 22651271
chr_1 g12344 g12344.t13 exon g12344.t13.exon2 22651340 22651520
chr_1 g12344 g12344.t13 cds g12344.t13.CDS2 22651340 22651520
chr_1 g12344 g12344.t13 exon g12344.t13.exon3 22651603 22652260
chr_1 g12344 g12344.t13 cds g12344.t13.CDS3 22651603 22652260
chr_1 g12344 g12344.t13 exon g12344.t13.exon4 22652316 22652413
chr_1 g12344 g12344.t13 cds g12344.t13.CDS4 22652316 22652413
chr_1 g12344 g12344.t13 TTS g12344.t13 22652547 22652547

Sequences

>g12344.t13 Gene=g12344 Length=1603
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGGTAAGTAGAGAAAAGAAGAAAGCAT
TTTGTTGCTAGGGAAAATGTGTTTTGCATTTCATCATTTCAAATTAGTATTTCTGTGACA
ATTAAACGATACACACTCTTTTATTTTATTTTATCCATCGTATAAACATTTTCTCTGTAT
AATTTAGTATTCGGACTAAGCTAAAGATGTCGTATAGTTCTTCATTATCTTCTATGCCAA
TGTAAAAATCATAAAACTACAAAGTTCAAACTTTTATTGAACAAAAAAATTAAAAAAAAC
TAGTTTTTAAAAATTCCATTCATTAAAAGCAAACTAGATTATAATTACTAATCGCATCAT
GACATTGTGAAACATGTGATAGGAACGATTGAGGGCTTTAATTGAGTTGAAAAACATATT
TTTATTCATTTCCCAGTTACTATTCAAGTGCAATAGTAGACAAAAACAAAATTATTTTTA
ATCATAACACAATTGAATCATGTTTTCGAGACGCTATTTGTTACGAGTTTCCGTCACTTG
CTTATTTACAAATAACAGCAATTACGTACTTTCTCATTATAACATTACTAGACATAAGAT
TAATCTATGTCAAAATATTTCCACAATTGGCAAATTTCATGCAAAATTAAATGTTCAGTT
GAAAAGTCCAGAGCCAATAGAAGCTAAAATAATTGATGGAAAGAAGATTTCTGAAGAAAT
TAAGATTGAATTACGCGAACAGATTAAAGAATGGATGCAACAAGAAAATGTAAGAGCTCC
TCAATTGACATGCATTTTGGTTGGCGAAGATTCAGCTTCACAAGTCTATGTGAAGAATAA
AATGAAAGCCGCAAATGATGTCGGAATAAAGAGTGAAACAATAAATTTACCAAAAACAAT
AAGTGAAGATGAACTTATTCAAATAATTGAGAGACTCAATGATGACAATTCAGTTGATGG
AATTTTAGTTCAACTTCCATTGCCTGATCATATTGATGATAAAAAGATTTGCAATATTGT
GAGTTGTGAGAAAGATGTTGATGGATTTAATAGTACTAATCTTGGACGTTTGAGTCAAGA
CTTGAATACTATGGTACCTTGTACACCACTCGGTGTTCAAGAGCTTTTAAAAAAATATGA
TATCGAAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAAGTGCACATGTTGGAAAGCC
AATTCAATCTCTATTGCAATCTGATGGTCGTCATGAAATTTCAGGAATGGATTGCACAAC
TATAATGTGTCACAGATTCACACCTCCAGAGAAACTTAAAAAATTTTGCAGAGAAGCTGA
TATTATCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTGAAGATATGATTAAGCCAGG
TGCTTGTGTTATTGATGTCGGTATTACAAGAATCTATGATGAAGAGACTAAAAAATCAAA
GCTTGTTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTGCTGGTTTAATTACACCTGT
TCCAGGTGGAGTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAGCAGC
AAAGAGACTTGCAAAATTACGCAAAGAGAAGCTAATTAAATAA

>g12344.t13 Gene=g12344 Length=367
MFSRRYLLRVSVTCLFTNNSNYVLSHYNITRHKINLCQNISTIGKFHAKLNVQLKSPEPI
EAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGEDSASQVYVKNKMKAAND
VGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDHIDDKKICNIVSCEKDV
DGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVVVGRSAHVGKPIQSLLQ
SDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPNLIREDMIKPGACVIDV
GITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGGVGPMTVCMLMKNTFTAAKRLAKL
RKEKLIK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g12344.t13 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 177 355 2.91643E-84
15 g12344.t13 Gene3D G3DSA:3.40.50.720 - 65 334 1.7E-107
16 g12344.t13 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 67 351 1.7E-107
5 g12344.t13 Hamap MF_01576 Bifunctional protein FolD [folD]. 62 358 36.726048
3 g12344.t13 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 62 363 2.9E-132
4 g12344.t13 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 62 363 2.9E-132
9 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 94 116 1.5E-79
8 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 135 162 1.5E-79
7 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 170 191 1.5E-79
11 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 215 235 1.5E-79
12 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 274 303 1.5E-79
10 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 314 330 1.5E-79
6 g12344.t13 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 331 349 1.5E-79
2 g12344.t13 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 64 181 4.1E-40
1 g12344.t13 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 185 356 1.1E-65
18 g12344.t13 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
19 g12344.t13 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
20 g12344.t13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 17 -
21 g12344.t13 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 25 -
17 g12344.t13 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 367 -
23 g12344.t13 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 136 161 -
24 g12344.t13 ProSitePatterns PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. 335 343 -
14 g12344.t13 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 62 182 3.17E-40
13 g12344.t13 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 183 355 1.65E-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