Gene loci information

Transcript annotation

  • This transcript has been annotated as C-1-tetrahydrofolate synthase, cytoplasmic.

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_4 g15282 g15282.t4 TSS g15282.t4 4817326 4817326
chr_4 g15282 g15282.t4 isoform g15282.t4 4817464 4823040
chr_4 g15282 g15282.t4 exon g15282.t4.exon1 4817464 4817510
chr_4 g15282 g15282.t4 cds g15282.t4.CDS1 4817464 4817510
chr_4 g15282 g15282.t4 exon g15282.t4.exon2 4819526 4819736
chr_4 g15282 g15282.t4 cds g15282.t4.CDS2 4819526 4819736
chr_4 g15282 g15282.t4 exon g15282.t4.exon3 4819812 4820283
chr_4 g15282 g15282.t4 cds g15282.t4.CDS3 4819812 4820283
chr_4 g15282 g15282.t4 exon g15282.t4.exon4 4822052 4822617
chr_4 g15282 g15282.t4 cds g15282.t4.CDS4 4822052 4822617
chr_4 g15282 g15282.t4 exon g15282.t4.exon5 4822676 4822699
chr_4 g15282 g15282.t4 cds g15282.t4.CDS5 4822676 4822699
chr_4 g15282 g15282.t4 exon g15282.t4.exon6 4822761 4823040
chr_4 g15282 g15282.t4 cds g15282.t4.CDS6 4822761 4823039
chr_4 g15282 g15282.t4 TTS g15282.t4 NA NA

Sequences

>g15282.t4 Gene=g15282 Length=1600
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
AGATTGAATATTGATCCTAATAAGGTTGTTTGGCAAAGAG

>g15282.t4 Gene=g15282 Length=533
MLEEEAKILSGNEVSKEIRESLKRRVNELNKKLPNFRPGLAIIQVGGREDSNVYIRMKMK
AAAEIGIHAEHIQLPKTITESALLAKIEHLNMNSRFHGIIVQMPLDSCNKIDSHLITDSV
LPEKDVDGLNTVNEGKIAVGDLSGFLPCTPNGVVELIKRTGLGITGKEVVVLGRSRIVGT
PAAELLKWNHATVTVCHSKTENLKEVTARADVLVVAIGQPEMVKGDWVKKGAVVIDCGIN
AIPDPTKKVGQKLVGDVDFEQCKKVASYITPVPGGVGPMTVAMLMSNTVQSAERFAERLM
DTKWKICPLSLQIQSPVPSDIEISRSQEPKNISVLANEVGLLPGEVSLYGTRKAKISLNV
LDRLKDQEVGKYVVVAGITPTPLGEGKSTTMIGLAQALTGHRDKNAFATMRQPSQGPTFG
IKGGAAGGGYSQVIPMEDFNLHLTGDIHAVTAANNLLAAQLDARMFHEATQTDQALYDRL
VPTMRGERKFSAIQLRRLERLGINKTDPNSLTVEEISKFARLNIDPNKVVWQR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g15282.t4 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 122 293 1.58206E-95
21 g15282.t4 Coils Coil Coil 12 32 -
17 g15282.t4 Gene3D G3DSA:3.40.50.720 - 9 272 4.8E-104
19 g15282.t4 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 11 289 4.8E-104
18 g15282.t4 Gene3D G3DSA:3.40.50.300 - 316 468 9.7E-60
20 g15282.t4 Gene3D G3DSA:1.10.8.770 - 469 532 4.6E-31
6 g15282.t4 Hamap MF_01576 Bifunctional protein FolD [folD]. 6 296 35.427147
4 g15282.t4 PANTHER PTHR48099:SF5 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC 3 533 1.8E-254
5 g15282.t4 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 3 533 1.8E-254
9 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 38 60 3.0E-76
13 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 79 106 3.0E-76
8 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 116 137 3.0E-76
7 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 162 182 3.0E-76
12 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 211 240 3.0E-76
11 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 252 268 3.0E-76
10 g15282.t4 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 269 287 3.0E-76
2 g15282.t4 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 8 127 3.0E-35
1 g15282.t4 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 131 294 3.5E-67
3 g15282.t4 Pfam PF01268 Formate–tetrahydrofolate ligase 319 533 9.2E-72
24 g15282.t4 ProSitePatterns PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. 273 281 -
23 g15282.t4 ProSitePatterns PS00721 Formate–tetrahydrofolate ligase signature 1. 420 430 -
15 g15282.t4 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 6 128 4.32E-36
14 g15282.t4 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 130 294 4.2E-53
16 g15282.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 320 533 2.83E-58

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

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