General information for g15282.t8
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.t8 | isoform | g15282.t8 | 4822052 | 4824480 |
| chr_4 | g15282 | g15282.t8 | exon | g15282.t8.exon1 | 4822052 | 4822617 |
| chr_4 | g15282 | g15282.t8 | cds | g15282.t8.CDS1 | 4822156 | 4822617 |
| chr_4 | g15282 | g15282.t8 | exon | g15282.t8.exon2 | 4822676 | 4822699 |
| chr_4 | g15282 | g15282.t8 | cds | g15282.t8.CDS2 | 4822676 | 4822699 |
| chr_4 | g15282 | g15282.t8 | exon | g15282.t8.exon3 | 4822761 | 4823040 |
| chr_4 | g15282 | g15282.t8 | cds | g15282.t8.CDS3 | 4822761 | 4823040 |
| chr_4 | g15282 | g15282.t8 | exon | g15282.t8.exon4 | 4823097 | 4823614 |
| chr_4 | g15282 | g15282.t8 | cds | g15282.t8.CDS4 | 4823097 | 4823614 |
| chr_4 | g15282 | g15282.t8 | exon | g15282.t8.exon5 | 4823678 | 4823702 |
| chr_4 | g15282 | g15282.t8 | cds | g15282.t8.CDS5 | 4823678 | 4823702 |
| chr_4 | g15282 | g15282.t8 | exon | g15282.t8.exon6 | 4823810 | 4824480 |
| chr_4 | g15282 | g15282.t8 | cds | g15282.t8.CDS6 | 4823810 | 4824480 |
| chr_4 | g15282 | g15282.t8 | TTS | g15282.t8 | 4824543 | 4824543 |
| chr_4 | g15282 | g15282.t8 | TSS | g15282.t8 | NA | NA |
Sequences
>g15282.t8 Gene=g15282 Length=2084
ATCCAACTAAAAAAGTAGGCCAAAAACTGGTCGGTGATGTTGATTTTGAACAATGTAAAA
AAGTGGCTTCCTATATCACTCCAGTTCCAGGTGGTGTTGGTCCAATGACAGTAGCAATGT
TAATGTCCAACACAGTTCAATCAGCTGAACGTTTTGCAGAACGCCTAATGGATACAAAAT
GGAAAATTTGTCCCCTTTCACTTCAAATTCAATCACCAGTTCCATCAGATATTGAAATTT
CTCGATCACAAGAGCCAAAAAATATTTCAGTTTTAGCAAATGAAGTTGGTCTTTTGCCTG
GTGAAGTTTCACTTTATGGCACAAGAAAGGCAAAAATTTCTCTCAATGTTTTAGATCGAT
TGAAGGATCAAGAAGTTGGAAAATATGTAGTTGTAGCTGGCATCACACCCACACCACTTG
GTGAAGGCAAAAGTACAACTATGATTGGTCTTGCTCAAGCATTGACAGGTCATCGTGATA
AAAATGCTTTTGCAACAATGCGACAGCCATCACAAGGACCAACTTTTGGTATTAAAGGTG
GTGCTGCTGGTGGTGGTTATTCACAAGTCATACCAATGGAAGATTTCAATCTTCATTTAA
CAGGCGATATTCATGCAGTAACAGCAGCTAATAATTTACTCGCAGCTCAACTTGATGCTC
GTATGTTTCATGAAGCAACTCAAACTGATCAAGCTCTTTATGATCGTCTTGTACCAACAA
TGCGTGGTGAAAGAAAATTTTCAGCAATTCAATTGAGACGATTAGAAAGATTGGGAATTA
ACAAAACAGATCCAAATTCATTGACAGTTGAGGAAATTTCCAAATTTGCTAGATTGAATA
TTGATCCTAATAAGGTTGTTTGGCAAAGAGTCATGGACATCAACGACAGATATTTACGAA
AAATCACAATTGGTCAATCACCAACTGAGAAAAATTTCACTCGTGTTGAATCATTTTCAA
TTTCTGTTGCATCAGAAATTATGGCAATTTTGGCTCTTGCTACAAGTTTGGAAGATATGA
AAAATCGTATGGCAAGAATGGTTGTTGCATTTTCACGCAATGGCACGCCAATAACTGCTG
ATGATCTTGGCATGACTGGTGCATTAATGGTTTTAATGAAAGATGCAATTGAGCCAACAA
TGATGCAAACACTTGAAGGTACACCAGTTTTGGTTCATGCTGGTCCATTTGCAAATATTG
CTCATGGTTGCAATTCGGTTTTGGCTGATCAAATTGCATTAAAATTGGTTGGTAAAGATG
GATATGTTGTGACTGAAGCTGGTTTTGGAAGTGACATTGGAATGGAGAAATTTTTCAATA
TTAAATGTCGTGCATCTGGAATGAAACCTAATGCTGTTGTTTTAGTTGCTACTGTTCGTG
CATTAAAGATGCACGGTGGTGGACCAGCCGTAGTTTCAGGTTCTCCATTAAAGGATGAAT
ACACACAAGAAAATCTGACACTCGTTAAAGAAGGTCTTTGCAATTTAATCAGACATATTG
AAAATGTTCGCAAATATGGAATTCCTGTAATTGTCGCAATTAACGCTCATAAAAACGACA
CAGAAGCTGAACATGAATTGATCAAAAAAGGAGCAATAGAAAATGGTGCTTTTGCTTGTG
TAACTTCAAATCATTGGGCAGAAGGTGGAAAAGGTGCAGTTGATCTTGCTGATGCTTTAA
TTGAAGCTTGTAAACAACCAAACAGTGATTTCAAATTTCTTTATGAACTTGATTTGTCAA
TTGAAGAAAAAATCAATCGCATTGCAAAAGAAATGTATGGAGCAGGAAATGTTGAGTTCT
CACAAAAAGTTCGTGAAACTATGCGACTTTATGCTGAAAAAGGTTACTCAAAACTTCCAA
TTTGTATGGCAAAAACTTCAGCTTCACTCACTGGTGACCCAAATATCAAAGGTGCACCAA
ATGGTTTTAGAATTTTCGTCAATGACATGTTTTTGAGTGCTGGTGCTGGATTTATTGTGC
CATTAGTCGGTGAAATTTCAAGAATGCCTGGCTTACCAACTCGTCCGGCTATTTTTGATA
TTGATTTGAATACTGAAACTGGTGAAATGATTGGATTATTTTAA
>g15282.t8 Gene=g15282 Length=659
MTVAMLMSNTVQSAERFAERLMDTKWKICPLSLQIQSPVPSDIEISRSQEPKNISVLANE
VGLLPGEVSLYGTRKAKISLNVLDRLKDQEVGKYVVVAGITPTPLGEGKSTTMIGLAQAL
TGHRDKNAFATMRQPSQGPTFGIKGGAAGGGYSQVIPMEDFNLHLTGDIHAVTAANNLLA
AQLDARMFHEATQTDQALYDRLVPTMRGERKFSAIQLRRLERLGINKTDPNSLTVEEISK
FARLNIDPNKVVWQRVMDINDRYLRKITIGQSPTEKNFTRVESFSISVASEIMAILALAT
SLEDMKNRMARMVVAFSRNGTPITADDLGMTGALMVLMKDAIEPTMMQTLEGTPVLVHAG
PFANIAHGCNSVLADQIALKLVGKDGYVVTEAGFGSDIGMEKFFNIKCRASGMKPNAVVL
VATVRALKMHGGGPAVVSGSPLKDEYTQENLTLVKEGLCNLIRHIENVRKYGIPVIVAIN
AHKNDTEAEHELIKKGAIENGAFACVTSNHWAEGGKGAVDLADALIEACKQPNSDFKFLY
ELDLSIEEKINRIAKEMYGAGNVEFSQKVRETMRLYAEKGYSKLPICMAKTSASLTGDPN
IKGAPNGFRIFVNDMFLSAGAGFIVPLVGEISRMPGLPTRPAIFDIDLNTETGEMIGLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g15282.t8 | CDD | cd00477 | FTHFS | 54 | 658 | 0.0 |
| 7 | g15282.t8 | Gene3D | G3DSA:1.10.8.770 | - | 190 | 249 | 6.2E-31 |
| 6 | g15282.t8 | Gene3D | G3DSA:3.10.410.10 | Formyltetrahydrofolate synthetase | 545 | 634 | 1.2E-32 |
| 4 | g15282.t8 | Hamap | MF_01543 | Formate–tetrahydrofolate ligase [fhs]. | 39 | 659 | 41.785744 |
| 2 | g15282.t8 | PANTHER | PTHR48099:SF12 | MONOFUNCTIONAL C1-TETRAHYDROFOLATE SYNTHASE, MITOCHONDRIAL | 2 | 652 | 0.0 |
| 3 | g15282.t8 | PANTHER | PTHR48099 | C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED | 2 | 652 | 0.0 |
| 1 | g15282.t8 | Pfam | PF01268 | Formate–tetrahydrofolate ligase | 41 | 659 | 1.5E-255 |
| 9 | g15282.t8 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 283 | - |
| 10 | g15282.t8 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 284 | 302 | - |
| 8 | g15282.t8 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 303 | 659 | - |
| 13 | g15282.t8 | ProSitePatterns | PS00721 | Formate–tetrahydrofolate ligase signature 1. | 142 | 152 | - |
| 12 | g15282.t8 | ProSitePatterns | PS00722 | Formate–tetrahydrofolate ligase signature 2. | 421 | 432 | - |
| 5 | g15282.t8 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 42 | 655 | 5.04E-225 |
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:0005524 | ATP binding | MF |
| GO:0004329 | formate-tetrahydrofolate ligase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01938 (formate–tetrahydrofolate ligase)
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