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.t9 TSS g12344.t9 22650458 22650458
chr_1 g12344 g12344.t9 isoform g12344.t9 22650606 22652413
chr_1 g12344 g12344.t9 exon g12344.t9.exon1 22650606 22651271
chr_1 g12344 g12344.t9 cds g12344.t9.CDS1 22651105 22651271
chr_1 g12344 g12344.t9 exon g12344.t9.exon2 22651340 22651520
chr_1 g12344 g12344.t9 cds g12344.t9.CDS2 22651340 22651520
chr_1 g12344 g12344.t9 exon g12344.t9.exon3 22651603 22652264
chr_1 g12344 g12344.t9 cds g12344.t9.CDS3 22651603 22652264
chr_1 g12344 g12344.t9 exon g12344.t9.exon4 22652316 22652413
chr_1 g12344 g12344.t9 cds g12344.t9.CDS4 22652316 22652409
chr_1 g12344 g12344.t9 TTS g12344.t9 22652547 22652547

Sequences

>g12344.t9 Gene=g12344 Length=1607
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
TCCAGGTTTGTGGAGTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAG
CAGCAAAGAGACTTGCAAAATTACGCAAAGAGAAGCTAATTAAATAA

>g12344.t9 Gene=g12344 Length=367
MFSRRYLLRVSVTCLFTNNSNYVLSHYNITRHKINLCQNISTIGKFHAKLNVQLKSPEPI
EAKIIDGKKISEEIKIELREQIKEWMQQENVRAPQLTCILVGEDSASQVYVKNKMKAAND
VGIKSETINLPKTISEDELIQIIERLNDDNSVDGILVQLPLPDHIDDKKICNIVSCEKDV
DGFNSTNLGRLSQDLNTMVPCTPLGVQELLKKYDIETFGKTAVVVGRSAHVGKPIQSLLQ
SDGRHEISGMDCTTIMCHRFTPPEKLKKFCREADIIIVAVGKPNLIREDMIKPGACVIDV
GITRIYDEETKKSKLVGDVDFENVKKVAGLITPVPGLWSWSNDSLHADEEHIYSSKETCK
ITQREAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g12344.t9 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 177 336 1.18687E-70
15 g12344.t9 Gene3D G3DSA:3.40.50.720 - 65 334 4.3E-96
16 g12344.t9 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 67 336 4.3E-96
5 g12344.t9 Hamap MF_01576 Bifunctional protein FolD [folD]. 62 358 32.51368
3 g12344.t9 PANTHER PTHR48099:SF11 BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL 62 336 3.6E-117
4 g12344.t9 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 62 336 3.6E-117
9 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 94 116 9.1E-67
8 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 135 162 9.1E-67
7 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 170 191 9.1E-67
11 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 215 235 9.1E-67
12 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 274 303 9.1E-67
10 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 314 330 9.1E-67
6 g12344.t9 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 331 349 9.1E-67
2 g12344.t9 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 64 181 4.1E-40
1 g12344.t9 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 185 336 2.6E-53
18 g12344.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
19 g12344.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
20 g12344.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 17 -
21 g12344.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 25 -
17 g12344.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 367 -
23 g12344.t9 ProSitePatterns PS00766 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. 136 161 -
14 g12344.t9 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 62 182 3.17E-40
13 g12344.t9 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 183 336 5.96E-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.

Raw TPM values