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.t6 TSS g15282.t6 4819317 4819317
chr_4 g15282 g15282.t6 isoform g15282.t6 4819520 4822111
chr_4 g15282 g15282.t6 exon g15282.t6.exon1 4819520 4819736
chr_4 g15282 g15282.t6 cds g15282.t6.CDS1 4819647 4819736
chr_4 g15282 g15282.t6 exon g15282.t6.exon2 4819812 4820283
chr_4 g15282 g15282.t6 cds g15282.t6.CDS2 4819812 4820283
chr_4 g15282 g15282.t6 exon g15282.t6.exon3 4822052 4822111
chr_4 g15282 g15282.t6 cds g15282.t6.CDS3 4822052 4822110
chr_4 g15282 g15282.t6 TTS g15282.t6 NA NA

Sequences

>g15282.t6 Gene=g15282 Length=749
TTCTAGAGAGATTCGTGAATCTCTAAAACGTCGTGTCAATGAACTCAACAAGAAACTTCC
AAATTTTCGTCCAGGTCTTGCAATTATTCAAGTCGGTGGTCGTGAAGACTCAAATGTCTA
CATTCGAATGAAAATGAAGGCAGCAGCTGAAATTGGAATCCACGCTGAGCACATTCAACT
GCCAAAAACCATAACGGAAAGCGCTTTATTGGCAAAGATTGAACATTTAAACATGAATTC
ACGTTTTCATGGAATAATTGTGCAAATGCCACTTGATTCATGTAATAAAATCGACTCGCA
TCTCATCACTGACTCAGTACTACCCGAGAAAGATGTTGATGGCCTTAACACTGTCAATGA
AGGAAAAATTGCAGTTGGCGACTTGTCTGGCTTTCTTCCATGTACACCAAATGGTGTAGT
TGAATTGATCAAACGAACTGGCTTAGGAATTACAGGCAAAGAAGTTGTCGTACTCGGTCG
ATCAAGAATTGTTGGAACACCAGCTGCTGAGTTGTTGAAATGGAATCATGCAACTGTGAC
AGTTTGTCATTCAAAGACAGAAAATTTGAAAGAAGTCACAGCAAGAGCTGATGTTCTTGT
TGTTGCTATAGGGCAACCCGAAATGGTTAAAGGCGATTGGGTGAAGAAAGGTGCTGTCGT
TATCGATTGTGGTATAAATGCTATTCCTGATCCAACTAAAAAAGTAGGCCAAAAACTGGT
CGGTGATGTTGATTTTGAACAATGTAAAA

>g15282.t6 Gene=g15282 Length=207
MKMKAAAEIGIHAEHIQLPKTITESALLAKIEHLNMNSRFHGIIVQMPLDSCNKIDSHLI
TDSVLPEKDVDGLNTVNEGKIAVGDLSGFLPCTPNGVVELIKRTGLGITGKEVVVLGRSR
IVGTPAAELLKWNHATVTVCHSKTENLKEVTARADVLVVAIGQPEMVKGDWVKKGAVVID
CGINAIPDPTKKVGQKLVGDVDFEQCK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g15282.t6 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 66 204 0
13 g15282.t6 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 1 64 0
12 g15282.t6 Gene3D G3DSA:3.40.50.720 - 85 207 0
3 g15282.t6 PANTHER PTHR48099:SF5 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC 1 206 0
4 g15282.t6 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 1 206 0
5 g15282.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 23 50 0
6 g15282.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 60 81 0
7 g15282.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 106 126 0
9 g15282.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 155 184 0
8 g15282.t6 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 196 207 0
2 g15282.t6 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 1 71 0
1 g15282.t6 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 75 206 0
11 g15282.t6 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 72 0
10 g15282.t6 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 74 205 0

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