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.t3 TSS g15282.t3 4817326 4817326
chr_4 g15282 g15282.t3 isoform g15282.t3 4817464 4822111
chr_4 g15282 g15282.t3 exon g15282.t3.exon1 4817464 4817510
chr_4 g15282 g15282.t3 cds g15282.t3.CDS1 4817464 4817510
chr_4 g15282 g15282.t3 exon g15282.t3.exon2 4819526 4819736
chr_4 g15282 g15282.t3 cds g15282.t3.CDS2 4819526 4819736
chr_4 g15282 g15282.t3 exon g15282.t3.exon3 4819812 4820283
chr_4 g15282 g15282.t3 cds g15282.t3.CDS3 4819812 4820283
chr_4 g15282 g15282.t3 exon g15282.t3.exon4 4822052 4822111
chr_4 g15282 g15282.t3 cds g15282.t3.CDS4 4822052 4822110
chr_4 g15282 g15282.t3 TTS g15282.t3 NA NA

Sequences

>g15282.t3 Gene=g15282 Length=790
ATGTTAGAAGAAGAAGCAAAAATTTTATCCGGAAATGAAGTCTCAAAAGAGATTCGTGAA
TCTCTAAAACGTCGTGTCAATGAACTCAACAAGAAACTTCCAAATTTTCGTCCAGGTCTT
GCAATTATTCAAGTCGGTGGTCGTGAAGACTCAAATGTCTACATTCGAATGAAAATGAAG
GCAGCAGCTGAAATTGGAATCCACGCTGAGCACATTCAACTGCCAAAAACCATAACGGAA
AGCGCTTTATTGGCAAAGATTGAACATTTAAACATGAATTCACGTTTTCATGGAATAATT
GTGCAAATGCCACTTGATTCATGTAATAAAATCGACTCGCATCTCATCACTGACTCAGTA
CTACCCGAGAAAGATGTTGATGGCCTTAACACTGTCAATGAAGGAAAAATTGCAGTTGGC
GACTTGTCTGGCTTTCTTCCATGTACACCAAATGGTGTAGTTGAATTGATCAAACGAACT
GGCTTAGGAATTACAGGCAAAGAAGTTGTCGTACTCGGTCGATCAAGAATTGTTGGAACA
CCAGCTGCTGAGTTGTTGAAATGGAATCATGCAACTGTGACAGTTTGTCATTCAAAGACA
GAAAATTTGAAAGAAGTCACAGCAAGAGCTGATGTTCTTGTTGTTGCTATAGGGCAACCC
GAAATGGTTAAAGGCGATTGGGTGAAGAAAGGTGCTGTCGTTATCGATTGTGGTATAAAT
GCTATTCCTGATCCAACTAAAAAAGTAGGCCAAAAACTGGTCGGTGATGTTGATTTTGAA
CAATGTAAAA

>g15282.t3 Gene=g15282 Length=263
MLEEEAKILSGNEVSKEIRESLKRRVNELNKKLPNFRPGLAIIQVGGREDSNVYIRMKMK
AAAEIGIHAEHIQLPKTITESALLAKIEHLNMNSRFHGIIVQMPLDSCNKIDSHLITDSV
LPEKDVDGLNTVNEGKIAVGDLSGFLPCTPNGVVELIKRTGLGITGKEVVVLGRSRIVGT
PAAELLKWNHATVTVCHSKTENLKEVTARADVLVVAIGQPEMVKGDWVKKGAVVIDCGIN
AIPDPTKKVGQKLVGDVDFEQCK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g15282.t3 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 122 260 3.06211E-71
16 g15282.t3 Coils Coil Coil 12 32 -
14 g15282.t3 Gene3D G3DSA:3.40.50.720 - 9 260 1.4E-86
15 g15282.t3 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 11 146 1.4E-86
5 g15282.t3 Hamap MF_01576 Bifunctional protein FolD [folD]. 6 263 26.065754
3 g15282.t3 PANTHER PTHR48099:SF5 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC 3 262 8.7E-107
4 g15282.t3 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 3 262 8.7E-107
8 g15282.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 38 60 4.1E-61
11 g15282.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 79 106 4.1E-61
7 g15282.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 116 137 4.1E-61
6 g15282.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 162 182 4.1E-61
10 g15282.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 211 240 4.1E-61
9 g15282.t3 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 252 263 4.1E-61
2 g15282.t3 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 8 127 7.1E-36
1 g15282.t3 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 131 262 1.6E-48
13 g15282.t3 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 6 128 9.59E-37
12 g15282.t3 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 130 261 2.03E-40

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