General information for g15282.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as C-1-tetrahydrofolate synthase, cytoplasmic.
Parent gene
- The parent gene g15282 is located on chr_4: 4823097..4824480 (+ 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_4 | g15282 | g15282.t1 | TSS | g15282.t1 | 4817326 | 4817326 |
| chr_4 | g15282 | g15282.t1 | isoform | g15282.t1 | 4817464 | 4824480 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon1 | 4817464 | 4817510 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS1 | 4817464 | 4817510 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon2 | 4819526 | 4819736 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS2 | 4819526 | 4819736 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon3 | 4819812 | 4820283 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS3 | 4819812 | 4820283 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon4 | 4822052 | 4822617 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS4 | 4822052 | 4822617 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon5 | 4822676 | 4822699 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS5 | 4822676 | 4822699 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon6 | 4822761 | 4823040 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS6 | 4822761 | 4823040 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon7 | 4823097 | 4823614 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS7 | 4823097 | 4823614 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon8 | 4823678 | 4823702 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS8 | 4823678 | 4823702 |
| chr_4 | g15282 | g15282.t1 | exon | g15282.t1.exon9 | 4823810 | 4824480 |
| chr_4 | g15282 | g15282.t1 | cds | g15282.t1.CDS9 | 4823810 | 4824480 |
| chr_4 | g15282 | g15282.t1 | TTS | g15282.t1 | 4824543 | 4824543 |
Sequences
>g15282.t1 Gene=g15282 Length=2814
ATGTTAGAAGAAGAAGCAAAAATTTTATCCGGAAATGAAGTCTCAAAAGAGATTCGTGAA
TCTCTAAAACGTCGTGTCAATGAACTCAACAAGAAACTTCCAAATTTTCGTCCAGGTCTT
GCAATTATTCAAGTCGGTGGTCGTGAAGACTCAAATGTCTACATTCGAATGAAAATGAAG
GCAGCAGCTGAAATTGGAATCCACGCTGAGCACATTCAACTGCCAAAAACCATAACGGAA
AGCGCTTTATTGGCAAAGATTGAACATTTAAACATGAATTCACGTTTTCATGGAATAATT
GTGCAAATGCCACTTGATTCATGTAATAAAATCGACTCGCATCTCATCACTGACTCAGTA
CTACCCGAGAAAGATGTTGATGGCCTTAACACTGTCAATGAAGGAAAAATTGCAGTTGGC
GACTTGTCTGGCTTTCTTCCATGTACACCAAATGGTGTAGTTGAATTGATCAAACGAACT
GGCTTAGGAATTACAGGCAAAGAAGTTGTCGTACTCGGTCGATCAAGAATTGTTGGAACA
CCAGCTGCTGAGTTGTTGAAATGGAATCATGCAACTGTGACAGTTTGTCATTCAAAGACA
GAAAATTTGAAAGAAGTCACAGCAAGAGCTGATGTTCTTGTTGTTGCTATAGGGCAACCC
GAAATGGTTAAAGGCGATTGGGTGAAGAAAGGTGCTGTCGTTATCGATTGTGGTATAAAT
GCTATTCCTGATCCAACTAAAAAAGTAGGCCAAAAACTGGTCGGTGATGTTGATTTTGAA
CAATGTAAAAAAGTGGCTTCCTATATCACTCCAGTTCCAGGTGGTGTTGGTCCAATGACA
GTAGCAATGTTAATGTCCAACACAGTTCAATCAGCTGAACGTTTTGCAGAACGCCTAATG
GATACAAAATGGAAAATTTGTCCCCTTTCACTTCAAATTCAATCACCAGTTCCATCAGAT
ATTGAAATTTCTCGATCACAAGAGCCAAAAAATATTTCAGTTTTAGCAAATGAAGTTGGT
CTTTTGCCTGGTGAAGTTTCACTTTATGGCACAAGAAAGGCAAAAATTTCTCTCAATGTT
TTAGATCGATTGAAGGATCAAGAAGTTGGAAAATATGTAGTTGTAGCTGGCATCACACCC
ACACCACTTGGTGAAGGCAAAAGTACAACTATGATTGGTCTTGCTCAAGCATTGACAGGT
CATCGTGATAAAAATGCTTTTGCAACAATGCGACAGCCATCACAAGGACCAACTTTTGGT
ATTAAAGGTGGTGCTGCTGGTGGTGGTTATTCACAAGTCATACCAATGGAAGATTTCAAT
CTTCATTTAACAGGCGATATTCATGCAGTAACAGCAGCTAATAATTTACTCGCAGCTCAA
CTTGATGCTCGTATGTTTCATGAAGCAACTCAAACTGATCAAGCTCTTTATGATCGTCTT
GTACCAACAATGCGTGGTGAAAGAAAATTTTCAGCAATTCAATTGAGACGATTAGAAAGA
TTGGGAATTAACAAAACAGATCCAAATTCATTGACAGTTGAGGAAATTTCCAAATTTGCT
AGATTGAATATTGATCCTAATAAGGTTGTTTGGCAAAGAGTCATGGACATCAACGACAGA
TATTTACGAAAAATCACAATTGGTCAATCACCAACTGAGAAAAATTTCACTCGTGTTGAA
TCATTTTCAATTTCTGTTGCATCAGAAATTATGGCAATTTTGGCTCTTGCTACAAGTTTG
GAAGATATGAAAAATCGTATGGCAAGAATGGTTGTTGCATTTTCACGCAATGGCACGCCA
ATAACTGCTGATGATCTTGGCATGACTGGTGCATTAATGGTTTTAATGAAAGATGCAATT
GAGCCAACAATGATGCAAACACTTGAAGGTACACCAGTTTTGGTTCATGCTGGTCCATTT
GCAAATATTGCTCATGGTTGCAATTCGGTTTTGGCTGATCAAATTGCATTAAAATTGGTT
GGTAAAGATGGATATGTTGTGACTGAAGCTGGTTTTGGAAGTGACATTGGAATGGAGAAA
TTTTTCAATATTAAATGTCGTGCATCTGGAATGAAACCTAATGCTGTTGTTTTAGTTGCT
ACTGTTCGTGCATTAAAGATGCACGGTGGTGGACCAGCCGTAGTTTCAGGTTCTCCATTA
AAGGATGAATACACACAAGAAAATCTGACACTCGTTAAAGAAGGTCTTTGCAATTTAATC
AGACATATTGAAAATGTTCGCAAATATGGAATTCCTGTAATTGTCGCAATTAACGCTCAT
AAAAACGACACAGAAGCTGAACATGAATTGATCAAAAAAGGAGCAATAGAAAATGGTGCT
TTTGCTTGTGTAACTTCAAATCATTGGGCAGAAGGTGGAAAAGGTGCAGTTGATCTTGCT
GATGCTTTAATTGAAGCTTGTAAACAACCAAACAGTGATTTCAAATTTCTTTATGAACTT
GATTTGTCAATTGAAGAAAAAATCAATCGCATTGCAAAAGAAATGTATGGAGCAGGAAAT
GTTGAGTTCTCACAAAAAGTTCGTGAAACTATGCGACTTTATGCTGAAAAAGGTTACTCA
AAACTTCCAATTTGTATGGCAAAAACTTCAGCTTCACTCACTGGTGACCCAAATATCAAA
GGTGCACCAAATGGTTTTAGAATTTTCGTCAATGACATGTTTTTGAGTGCTGGTGCTGGA
TTTATTGTGCCATTAGTCGGTGAAATTTCAAGAATGCCTGGCTTACCAACTCGTCCGGCT
ATTTTTGATATTGATTTGAATACTGAAACTGGTGAAATGATTGGATTATTTTAA
>g15282.t1 Gene=g15282 Length=937
MLEEEAKILSGNEVSKEIRESLKRRVNELNKKLPNFRPGLAIIQVGGREDSNVYIRMKMK
AAAEIGIHAEHIQLPKTITESALLAKIEHLNMNSRFHGIIVQMPLDSCNKIDSHLITDSV
LPEKDVDGLNTVNEGKIAVGDLSGFLPCTPNGVVELIKRTGLGITGKEVVVLGRSRIVGT
PAAELLKWNHATVTVCHSKTENLKEVTARADVLVVAIGQPEMVKGDWVKKGAVVIDCGIN
AIPDPTKKVGQKLVGDVDFEQCKKVASYITPVPGGVGPMTVAMLMSNTVQSAERFAERLM
DTKWKICPLSLQIQSPVPSDIEISRSQEPKNISVLANEVGLLPGEVSLYGTRKAKISLNV
LDRLKDQEVGKYVVVAGITPTPLGEGKSTTMIGLAQALTGHRDKNAFATMRQPSQGPTFG
IKGGAAGGGYSQVIPMEDFNLHLTGDIHAVTAANNLLAAQLDARMFHEATQTDQALYDRL
VPTMRGERKFSAIQLRRLERLGINKTDPNSLTVEEISKFARLNIDPNKVVWQRVMDINDR
YLRKITIGQSPTEKNFTRVESFSISVASEIMAILALATSLEDMKNRMARMVVAFSRNGTP
ITADDLGMTGALMVLMKDAIEPTMMQTLEGTPVLVHAGPFANIAHGCNSVLADQIALKLV
GKDGYVVTEAGFGSDIGMEKFFNIKCRASGMKPNAVVLVATVRALKMHGGGPAVVSGSPL
KDEYTQENLTLVKEGLCNLIRHIENVRKYGIPVIVAINAHKNDTEAEHELIKKGAIENGA
FACVTSNHWAEGGKGAVDLADALIEACKQPNSDFKFLYELDLSIEEKINRIAKEMYGAGN
VEFSQKVRETMRLYAEKGYSKLPICMAKTSASLTGDPNIKGAPNGFRIFVNDMFLSAGAG
FIVPLVGEISRMPGLPTRPAIFDIDLNTETGEMIGLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g15282.t1 | CDD | cd01080 | NAD_bind_m-THF_DH_Cyclohyd | 122 | 293 | 8.85123E-92 |
| 27 | g15282.t1 | CDD | cd00477 | FTHFS | 332 | 936 | 0.0 |
| 22 | g15282.t1 | Coils | Coil | Coil | 12 | 32 | - |
| 18 | g15282.t1 | Gene3D | G3DSA:3.40.50.720 | - | 9 | 272 | 1.7E-103 |
| 20 | g15282.t1 | Gene3D | G3DSA:3.40.50.10860 | Leucine Dehydrogenase | 11 | 289 | 1.7E-103 |
| 21 | g15282.t1 | Gene3D | G3DSA:1.10.8.770 | - | 469 | 527 | 9.8E-31 |
| 19 | g15282.t1 | Gene3D | G3DSA:3.10.410.10 | Formyltetrahydrofolate synthetase | 823 | 912 | 2.0E-32 |
| 6 | g15282.t1 | Hamap | MF_01576 | Bifunctional protein FolD [folD]. | 6 | 296 | 35.427147 |
| 7 | g15282.t1 | Hamap | MF_01543 | Formate–tetrahydrofolate ligase [fhs]. | 317 | 937 | 41.785744 |
| 4 | g15282.t1 | PANTHER | PTHR48099:SF1 | C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC | 5 | 930 | 0.0 |
| 5 | g15282.t1 | PANTHER | PTHR48099 | C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED | 5 | 930 | 0.0 |
| 10 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 38 | 60 | 6.5E-75 |
| 14 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 79 | 106 | 6.5E-75 |
| 9 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 116 | 137 | 6.5E-75 |
| 8 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 162 | 182 | 6.5E-75 |
| 13 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 211 | 240 | 6.5E-75 |
| 12 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 252 | 268 | 6.5E-75 |
| 11 | g15282.t1 | PRINTS | PR00085 | Tetrahydrofolate dehydrogenase/cyclohydrolase family signature | 269 | 287 | 6.5E-75 |
| 2 | g15282.t1 | Pfam | PF00763 | Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain | 8 | 127 | 7.2E-35 |
| 1 | g15282.t1 | Pfam | PF02882 | Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain | 131 | 294 | 9.3E-67 |
| 3 | g15282.t1 | Pfam | PF01268 | Formate–tetrahydrofolate ligase | 319 | 937 | 4.8E-255 |
| 24 | g15282.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 561 | - |
| 25 | g15282.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 562 | 580 | - |
| 23 | g15282.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 581 | 937 | - |
| 30 | g15282.t1 | ProSitePatterns | PS00767 | Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. | 273 | 281 | - |
| 29 | g15282.t1 | ProSitePatterns | PS00721 | Formate–tetrahydrofolate ligase signature 1. | 420 | 430 | - |
| 28 | g15282.t1 | ProSitePatterns | PS00722 | Formate–tetrahydrofolate ligase signature 2. | 699 | 710 | - |
| 16 | g15282.t1 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 6 | 128 | 1.06E-35 |
| 15 | g15282.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 130 | 294 | 1.32E-52 |
| 17 | g15282.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 320 | 933 | 1.7E-224 |
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:0005524 | ATP binding | MF |
| GO:0003824 | catalytic activity | MF |
| GO:0055114 | NA | NA |
| GO:0004329 | formate-tetrahydrofolate ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00288 (methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / formyltetrahydrofolate synthetase)
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