General information for g12344.t15
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial.
Parent gene
- The parent gene g12344 is located on chr_1: 22651653..22652413 (+ strand)
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.t15 | TSS | g12344.t15 | 22650458 | 22650458 |
| chr_1 | g12344 | g12344.t15 | isoform | g12344.t15 | 22650606 | 22652413 |
| chr_1 | g12344 | g12344.t15 | exon | g12344.t15.exon1 | 22650606 | 22651271 |
| chr_1 | g12344 | g12344.t15 | exon | g12344.t15.exon2 | 22651340 | 22651520 |
| chr_1 | g12344 | g12344.t15 | exon | g12344.t15.exon3 | 22651608 | 22652260 |
| chr_1 | g12344 | g12344.t15 | cds | g12344.t15.CDS1 | 22651846 | 22652260 |
| chr_1 | g12344 | g12344.t15 | exon | g12344.t15.exon4 | 22652316 | 22652413 |
| chr_1 | g12344 | g12344.t15 | cds | g12344.t15.CDS2 | 22652316 | 22652413 |
| chr_1 | g12344 | g12344.t15 | TTS | g12344.t15 | 22652547 | 22652547 |
Sequences
>g12344.t15 Gene=g12344 Length=1598
ATGGCACCAAATCCACATAGTGAAGTTCCATTACGGTAAGTAGAGAAAAGAAGAAAGCAT
TTTGTTGCTAGGGAAAATGTGTTTTGCATTTCATCATTTCAAATTAGTATTTCTGTGACA
ATTAAACGATACACACTCTTTTATTTTATTTTATCCATCGTATAAACATTTTCTCTGTAT
AATTTAGTATTCGGACTAAGCTAAAGATGTCGTATAGTTCTTCATTATCTTCTATGCCAA
TGTAAAAATCATAAAACTACAAAGTTCAAACTTTTATTGAACAAAAAAATTAAAAAAAAC
TAGTTTTTAAAAATTCCATTCATTAAAAGCAAACTAGATTATAATTACTAATCGCATCAT
GACATTGTGAAACATGTGATAGGAACGATTGAGGGCTTTAATTGAGTTGAAAAACATATT
TTTATTCATTTCCCAGTTACTATTCAAGTGCAATAGTAGACAAAAACAAAATTATTTTTA
ATCATAACACAATTGAATCATGTTTTCGAGACGCTATTTGTTACGAGTTTCCGTCACTTG
CTTATTTACAAATAACAGCAATTACGTACTTTCTCATTATAACATTACTAGACATAAGAT
TAATCTATGTCAAAATATTTCCACAATTGGCAAATTTCATGCAAAATTAAATGTTCAGTT
GAAAAGTCCAGAGCCAATAGAAGCTAAAATAATTGATGGAAAGAAGATTTCTGAAGAAAT
TAAGATTGAATTACGCGAACAGATTAAAGAATGGATGCAACAAGAAAATGTAAGAGCTCC
TCAATTGACATGCATTTTGGTTGGCGAAGATTCAGCTTCACAAGTCTATGTGAAGAATAA
AATGAAAAAATGATGTCGGAATAAAGAGTGAAACAATAAATTTACCAAAAACAATAAGTG
AAGATGAACTTATTCAAATAATTGAGAGACTCAATGATGACAATTCAGTTGATGGAATTT
TAGTTCAACTTCCATTGCCTGATCATATTGATGATAAAAAGATTTGCAATATTGTGAGTT
GTGAGAAAGATGTTGATGGATTTAATAGTACTAATCTTGGACGTTTGAGTCAAGACTTGA
ATACTATGGTACCTTGTACACCACTCGGTGTTCAAGAGCTTTTAAAAAAATATGATATCG
AAACATTCGGCAAAACTGCTGTCGTTGTTGGAAGAAGTGCACATGTTGGAAAGCCAATTC
AATCTCTATTGCAATCTGATGGTCGTCATGAAATTTCAGGAATGGATTGCACAACTATAA
TGTGTCACAGATTCACACCTCCAGAGAAACTTAAAAAATTTTGCAGAGAAGCTGATATTA
TCATTGTTGCCGTTGGAAAACCAAATTTAATTCGTGAAGATATGATTAAGCCAGGTGCTT
GTGTTATTGATGTCGGTATTACAAGAATCTATGATGAAGAGACTAAAAAATCAAAGCTTG
TTGGTGATGTTGATTTTGAAAATGTAAAGAAAGTTGCTGGTTTAATTACACCTGTTCCAG
GTGGAGTTGGTCCAATGACAGTTTGCATGCTGATGAAGAACACATTTACAGCAGCAAAGA
GACTTGCAAAATTACGCAAAGAGAAGCTAATTAAATAA
>g12344.t15 Gene=g12344 Length=170
MVPCTPLGVQELLKKYDIETFGKTAVVVGRSAHVGKPIQSLLQSDGRHEISGMDCTTIMC
HRFTPPEKLKKFCREADIIIVAVGKPNLIREDMIKPGACVIDVGITRIYDEETKKSKLVG
DVDFENVKKVAGLITPVPGGVGPMTVCMLMKNTFTAAKRLAKLRKEKLIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12344.t15 | CDD | cd01080 | NAD_bind_m-THF_DH_Cyclohyd | 2 | 158 | 1.07168E-72 |
| 10 | g12344.t15 | Gene3D | G3DSA:3.40.50.720 | - | 1 | 142 | 2.8E-55 |
| 2 | g12344.t15 | PANTHER | PTHR48099:SF11 | BIFUNCTIONAL METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE, MITOCHONDRIAL | 1 | 166 | 9.8E-72 |
| 3 | g12344.t15 | PANTHER | PTHR48099 | C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED | 1 | 166 | 9.8E-72 |
| 5 | g12344.t15 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 18 | 38 | 3.4E-44 |
| 4 | g12344.t15 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 77 | 106 | 3.4E-44 |
| 7 | g12344.t15 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 117 | 133 | 3.4E-44 |
| 6 | g12344.t15 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 134 | 152 | 3.4E-44 |
| 1 | g12344.t15 | Pfam | PF02882 | Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain | 1 | 159 | 1.9E-62 |
| 9 | g12344.t15 | ProSitePatterns | PS00767 | Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. | 138 | 146 | - |
| 8 | g12344.t15 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 2 | 158 | 4.64E-44 |
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.
