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.t7 TSS g15282.t7 4819317 4819317
chr_4 g15282 g15282.t7 isoform g15282.t7 4819520 4823163
chr_4 g15282 g15282.t7 exon g15282.t7.exon1 4819520 4819736
chr_4 g15282 g15282.t7 cds g15282.t7.CDS1 4819647 4819736
chr_4 g15282 g15282.t7 exon g15282.t7.exon2 4819812 4820283
chr_4 g15282 g15282.t7 cds g15282.t7.CDS2 4819812 4820283
chr_4 g15282 g15282.t7 exon g15282.t7.exon3 4822052 4822643
chr_4 g15282 g15282.t7 cds g15282.t7.CDS3 4822052 4822643
chr_4 g15282 g15282.t7 exon g15282.t7.exon4 4822761 4823040
chr_4 g15282 g15282.t7 cds g15282.t7.CDS4 4822761 4822770
chr_4 g15282 g15282.t7 exon g15282.t7.exon5 4823097 4823163
chr_4 g15282 g15282.t7 TTS g15282.t7 NA NA

Sequences

>g15282.t7 Gene=g15282 Length=1628
TTCTAGAGAGATTCGTGAATCTCTAAAACGTCGTGTCAATGAACTCAACAAGAAACTTCC
AAATTTTCGTCCAGGTCTTGCAATTATTCAAGTCGGTGGTCGTGAAGACTCAAATGTCTA
CATTCGAATGAAAATGAAGGCAGCAGCTGAAATTGGAATCCACGCTGAGCACATTCAACT
GCCAAAAACCATAACGGAAAGCGCTTTATTGGCAAAGATTGAACATTTAAACATGAATTC
ACGTTTTCATGGAATAATTGTGCAAATGCCACTTGATTCATGTAATAAAATCGACTCGCA
TCTCATCACTGACTCAGTACTACCCGAGAAAGATGTTGATGGCCTTAACACTGTCAATGA
AGGAAAAATTGCAGTTGGCGACTTGTCTGGCTTTCTTCCATGTACACCAAATGGTGTAGT
TGAATTGATCAAACGAACTGGCTTAGGAATTACAGGCAAAGAAGTTGTCGTACTCGGTCG
ATCAAGAATTGTTGGAACACCAGCTGCTGAGTTGTTGAAATGGAATCATGCAACTGTGAC
AGTTTGTCATTCAAAGACAGAAAATTTGAAAGAAGTCACAGCAAGAGCTGATGTTCTTGT
TGTTGCTATAGGGCAACCCGAAATGGTTAAAGGCGATTGGGTGAAGAAAGGTGCTGTCGT
TATCGATTGTGGTATAAATGCTATTCCTGATCCAACTAAAAAAGTAGGCCAAAAACTGGT
CGGTGATGTTGATTTTGAACAATGTAAAAAAGTGGCTTCCTATATCACTCCAGTTCCAGG
TGGTGTTGGTCCAATGACAGTAGCAATGTTAATGTCCAACACAGTTCAATCAGCTGAACG
TTTTGCAGAACGCCTAATGGATACAAAATGGAAAATTTGTCCCCTTTCACTTCAAATTCA
ATCACCAGTTCCATCAGATATTGAAATTTCTCGATCACAAGAGCCAAAAAATATTTCAGT
TTTAGCAAATGAAGTTGGTCTTTTGCCTGGTGAAGTTTCACTTTATGGCACAAGAAAGGC
AAAAATTTCTCTCAATGTTTTAGATCGATTGAAGGATCAAGAAGTTGGAAAATATGTAGT
TGTAGCTGGCATCACACCCACACCACTTGGTGAAGGCAAAAGTACAACTATGATTGGTCT
TGCTCAAGCATTGACAGGTCATCGTGATAAAAATGCTTTTGCAACAATGCGACAGCCATC
ACAAGGACCAACTTTTGGTATTAAAGGTGGTGCTGCTGGTGGTGGTTATTCACAAGTAAG
TCAAAAAAAATTTCCTAAAATCTTCATTTAACAGGCGATATTCATGCAGTAACAGCAGCT
AATAATTTACTCGCAGCTCAACTTGATGCTCGTATGTTTCATGAAGCAACTCAAACTGAT
CAAGCTCTTTATGATCGTCTTGTACCAACAATGCGTGGTGAAAGAAAATTTTCAGCAATT
CAATTGAGACGATTAGAAAGATTGGGAATTAACAAAACAGATCCAAATTCATTGACAGTT
GAGGAAATTTCCAAATTTGCTAGATTGAATATTGATCCTAATAAGGTTGTTTGGCAAAGA
GTCATGGACATCAACGACAGATATTTACGAAAAATCACAATTGGTCAATCACCAACTGAG
AAAAATTT

>g15282.t7 Gene=g15282 Length=387
MKMKAAAEIGIHAEHIQLPKTITESALLAKIEHLNMNSRFHGIIVQMPLDSCNKIDSHLI
TDSVLPEKDVDGLNTVNEGKIAVGDLSGFLPCTPNGVVELIKRTGLGITGKEVVVLGRSR
IVGTPAAELLKWNHATVTVCHSKTENLKEVTARADVLVVAIGQPEMVKGDWVKKGAVVID
CGINAIPDPTKKVGQKLVGDVDFEQCKKVASYITPVPGGVGPMTVAMLMSNTVQSAERFA
ERLMDTKWKICPLSLQIQSPVPSDIEISRSQEPKNISVLANEVGLLPGEVSLYGTRKAKI
SLNVLDRLKDQEVGKYVVVAGITPTPLGEGKSTTMIGLAQALTGHRDKNAFATMRQPSQG
PTFGIKGGAAGGGYSQVSQKKFPKIFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g15282.t7 CDD cd01080 NAD_bind_m-THF_DH_Cyclohyd 66 237 2.92657E-95
18 g15282.t7 Gene3D G3DSA:3.40.50.10860 Leucine Dehydrogenase 1 233 5.5E-88
16 g15282.t7 Gene3D G3DSA:3.40.50.720 - 91 216 5.5E-88
17 g15282.t7 Gene3D G3DSA:3.40.50.300 - 258 382 2.4E-50
6 g15282.t7 Hamap MF_01576 Bifunctional protein FolD [folD]. 1 240 26.024355
4 g15282.t7 PANTHER PTHR48099:SF5 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC 1 377 3.0E-173
5 g15282.t7 PANTHER PTHR48099 C-1-TETRAHYDROFOLATE SYNTHASE, CYTOPLASMIC-RELATED 1 377 3.0E-173
7 g15282.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 23 50 2.9E-65
10 g15282.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 60 81 2.9E-65
11 g15282.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 106 126 2.9E-65
12 g15282.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 155 184 2.9E-65
9 g15282.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 196 212 2.9E-65
8 g15282.t7 PRINTS PR00085 Tetrahydrofolate dehydrogenase/cyclohydrolase family signature 213 231 2.9E-65
2 g15282.t7 Pfam PF00763 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain 1 71 2.0E-18
1 g15282.t7 Pfam PF02882 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain 75 238 1.7E-67
3 g15282.t7 Pfam PF01268 Formate–tetrahydrofolate ligase 263 378 5.2E-46
21 g15282.t7 ProSitePatterns PS00767 Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. 217 225 -
20 g15282.t7 ProSitePatterns PS00721 Formate–tetrahydrofolate ligase signature 1. 364 374 -
14 g15282.t7 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain 1 72 8.25E-19
13 g15282.t7 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 74 238 1.84E-53
15 g15282.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 264 378 1.38E-37

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

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