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.t9 isoform g15282.t9 4822111 4823163
chr_4 g15282 g15282.t9 exon g15282.t9.exon1 4822111 4822617
chr_4 g15282 g15282.t9 cds g15282.t9.CDS1 4822156 4822617
chr_4 g15282 g15282.t9 exon g15282.t9.exon2 4822743 4823040
chr_4 g15282 g15282.t9 cds g15282.t9.CDS2 4822743 4823040
chr_4 g15282 g15282.t9 exon g15282.t9.exon3 4823097 4823163
chr_4 g15282 g15282.t9 cds g15282.t9.CDS3 4823097 4823161
chr_4 g15282 g15282.t9 TSS g15282.t9 NA NA
chr_4 g15282 g15282.t9 TTS g15282.t9 NA NA

Sequences

>g15282.t9 Gene=g15282 Length=872
AAAGTGGCTTCCTATATCACTCCAGTTCCAGGTGGTGTTGGTCCAATGACAGTAGCAATG
TTAATGTCCAACACAGTTCAATCAGCTGAACGTTTTGCAGAACGCCTAATGGATACAAAA
TGGAAAATTTGTCCCCTTTCACTTCAAATTCAATCACCAGTTCCATCAGATATTGAAATT
TCTCGATCACAAGAGCCAAAAAATATTTCAGTTTTAGCAAATGAAGTTGGTCTTTTGCCT
GGTGAAGTTTCACTTTATGGCACAAGAAAGGCAAAAATTTCTCTCAATGTTTTAGATCGA
TTGAAGGATCAAGAAGTTGGAAAATATGTAGTTGTAGCTGGCATCACACCCACACCACTT
GGTGAAGGCAAAAGTACAACTATGATTGGTCTTGCTCAAGCATTGACAGGTCATCGTGAT
AAAAATGCTTTTGCAACAATGCGACAGCCATCACAAGGACCAACTTTTGGTATTAAAGGT
GGTGCTGCTGGTGGTGGTTATTCACAATCTTTTTATAATTTCCAGCTTCATTTAACAGGC
GATATTCATGCAGTAACAGCAGCTAATAATTTACTCGCAGCTCAACTTGATGCTCGTATG
TTTCATGAAGCAACTCAAACTGATCAAGCTCTTTATGATCGTCTTGTACCAACAATGCGT
GGTGAAAGAAAATTTTCAGCAATTCAATTGAGACGATTAGAAAGATTGGGAATTAACAAA
ACAGATCCAAATTCATTGACAGTTGAGGAAATTTCCAAATTTGCTAGATTGAATATTGAT
CCTAATAAGGTTGTTTGGCAAAGAGTCATGGACATCAACGACAGATATTTACGAAAAATC
ACAATTGGTCAATCACCAACTGAGAAAAATTT

>g15282.t9 Gene=g15282 Length=275
MTVAMLMSNTVQSAERFAERLMDTKWKICPLSLQIQSPVPSDIEISRSQEPKNISVLANE
VGLLPGEVSLYGTRKAKISLNVLDRLKDQEVGKYVVVAGITPTPLGEGKSTTMIGLAQAL
TGHRDKNAFATMRQPSQGPTFGIKGGAAGGGYSQSFYNFQLHLTGDIHAVTAANNLLAAQ
LDARMFHEATQTDQALYDRLVPTMRGERKFSAIQLRRLERLGINKTDPNSLTVEEISKFA
RLNIDPNKVVWQRVMDINDRYLRKITIGQSPTEKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g15282.t9 Gene3D G3DSA:3.40.50.300 - 37 188 2.3E-53
7 g15282.t9 Gene3D G3DSA:1.10.8.770 - 189 252 1.6E-31
2 g15282.t9 PANTHER PTHR48099:SF12 MONOFUNCTIONAL C1-TETRAHYDROFOLATE SYNTHASE, MITOCHONDRIAL 2 271 3.2E-128
3 g15282.t9 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 2 271 3.2E-128
1 g15282.t9 Pfam PF01268 Formate–tetrahydrofolate ligase 41 274 1.4E-75
5 g15282.t9 ProSitePatterns PS00721 Formate–tetrahydrofolate ligase signature 1. 142 152 -
4 g15282.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 42 273 2.79E-61

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 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