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.t2 TSS g15282.t2 4817326 4817326
chr_4 g15282 g15282.t2 isoform g15282.t2 4817464 4820283
chr_4 g15282 g15282.t2 exon g15282.t2.exon1 4817464 4817510
chr_4 g15282 g15282.t2 cds g15282.t2.CDS1 4817464 4817510
chr_4 g15282 g15282.t2 exon g15282.t2.exon2 4819526 4819736
chr_4 g15282 g15282.t2 cds g15282.t2.CDS2 4819526 4819736
chr_4 g15282 g15282.t2 exon g15282.t2.exon3 4819812 4820283
chr_4 g15282 g15282.t2 cds g15282.t2.CDS3 4819812 4820282
chr_4 g15282 g15282.t2 TTS g15282.t2 NA NA

Sequences

>g15282.t2 Gene=g15282 Length=730
ATGTTAGAAGAAGAAGCAAAAATTTTATCCGGAAATGAAGTCTCAAAAGAGATTCGTGAA
TCTCTAAAACGTCGTGTCAATGAACTCAACAAGAAACTTCCAAATTTTCGTCCAGGTCTT
GCAATTATTCAAGTCGGTGGTCGTGAAGACTCAAATGTCTACATTCGAATGAAAATGAAG
GCAGCAGCTGAAATTGGAATCCACGCTGAGCACATTCAACTGCCAAAAACCATAACGGAA
AGCGCTTTATTGGCAAAGATTGAACATTTAAACATGAATTCACGTTTTCATGGAATAATT
GTGCAAATGCCACTTGATTCATGTAATAAAATCGACTCGCATCTCATCACTGACTCAGTA
CTACCCGAGAAAGATGTTGATGGCCTTAACACTGTCAATGAAGGAAAAATTGCAGTTGGC
GACTTGTCTGGCTTTCTTCCATGTACACCAAATGGTGTAGTTGAATTGATCAAACGAACT
GGCTTAGGAATTACAGGCAAAGAAGTTGTCGTACTCGGTCGATCAAGAATTGTTGGAACA
CCAGCTGCTGAGTTGTTGAAATGGAATCATGCAACTGTGACAGTTTGTCATTCAAAGACA
GAAAATTTGAAAGAAGTCACAGCAAGAGCTGATGTTCTTGTTGTTGCTATAGGGCAACCC
GAAATGGTTAAAGGCGATTGGGTGAAGAAAGGTGCTGTCGTTATCGATTGTGGTATAAAT
GCTATTCCTG

>g15282.t2 Gene=g15282 Length=243
MLEEEAKILSGNEVSKEIRESLKRRVNELNKKLPNFRPGLAIIQVGGREDSNVYIRMKMK
AAAEIGIHAEHIQLPKTITESALLAKIEHLNMNSRFHGIIVQMPLDSCNKIDSHLITDSV
LPEKDVDGLNTVNEGKIAVGDLSGFLPCTPNGVVELIKRTGLGITGKEVVVLGRSRIVGT
PAAELLKWNHATVTVCHSKTENLKEVTARADVLVVAIGQPEMVKGDWVKKGAVVIDCGIN
AIP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g15282.t2 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 122 243 8.61867E-64
15 g15282.t2 Coils Coil Coil 12 32 -
13 g15282.t2 Gene3D G3DSA:3.40.50.720 - 9 241 5.5E-83
14 g15282.t2 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 11 146 5.5E-83
5 g15282.t2 Hamap MF_01576 Bifunctional protein FolD [folD]. 6 242 23.535229
3 g15282.t2 PANTHER PTHR48099:SF1 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC 5 243 3.6E-99
4 g15282.t2 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 5 243 3.6E-99
8 g15282.t2 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 38 60 2.2E-54
10 g15282.t2 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 79 106 2.2E-54
7 g15282.t2 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 116 137 2.2E-54
6 g15282.t2 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 162 182 2.2E-54
9 g15282.t2 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 211 240 2.2E-54
2 g15282.t2 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 8 127 5.9E-36
1 g15282.t2 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 131 242 7.0E-44
12 g15282.t2 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 6 128 8.15E-37
11 g15282.t2 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 130 242 7.51E-36

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: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. There were no conditions that were differentially expressed