General information for g7542.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 5-formyltetrahydrofolate cyclo-ligase.
Parent gene
- The parent gene g7542 is located on chr_2: 24421035..24421856 (+ strand)
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_2 | g7542 | g7542.t1 | TSS | g7542.t1 | 24421017 | 24421017 |
| chr_2 | g7542 | g7542.t1 | isoform | g7542.t1 | 24421035 | 24421856 |
| chr_2 | g7542 | g7542.t1 | exon | g7542.t1.exon1 | 24421035 | 24421139 |
| chr_2 | g7542 | g7542.t1 | cds | g7542.t1.CDS1 | 24421035 | 24421139 |
| chr_2 | g7542 | g7542.t1 | exon | g7542.t1.exon2 | 24421218 | 24421331 |
| chr_2 | g7542 | g7542.t1 | cds | g7542.t1.CDS2 | 24421218 | 24421331 |
| chr_2 | g7542 | g7542.t1 | exon | g7542.t1.exon3 | 24421423 | 24421567 |
| chr_2 | g7542 | g7542.t1 | cds | g7542.t1.CDS3 | 24421423 | 24421567 |
| chr_2 | g7542 | g7542.t1 | exon | g7542.t1.exon4 | 24421624 | 24421856 |
| chr_2 | g7542 | g7542.t1 | cds | g7542.t1.CDS4 | 24421624 | 24421856 |
| chr_2 | g7542 | g7542.t1 | TTS | g7542.t1 | 24421929 | 24421929 |
Sequences
>g7542.t1 Gene=g7542 Length=597
ATGCAGAATCAATCGAAAGTTTTGCTAAGAAAAAGCATCAAGAGTTTAGTGCAACAGATA
ACTCCTGATAATAAATTAAGACAGTCAAATGCCATTATGGAGAAGCTTTTGAATATGTCT
GAATATAAAAACTCGTCTCGCATCTCGATATATCTGAGCACTGAAAATGAAGTTAACACC
ATTCCTATATTGACAACAATGTTTCAACAAAATAAGCAGGTATTCGTGCCAACATATGCA
GGAAGTGAAATGAAAATGGTAAAAGTGTTCGATATGAGGGATTATGAAAATTTACCAGTT
ACGAAATGGAAGATAAAACAACCAGATCCAGACGACAGCAGTCGAGAAAATCCCATGCTG
ACAGATCCATTAGACTTGATACTCTTGCCAGGCGTTGCATTTACGAGAAATGGTGATCGT
TTAGGACATGGAATGGGATATTATGATAAATATTTGCGAGAATATTTCAGCAGACATCCA
AATGTCAAGAATCATCACAAGACTCATCTCATTGGTTTAGCTTTTGAGGAGCAAATTGTT
GAGTCATTGCCGACAAATGAAAATGATTGGACTCTTGACTTGATATTGACAAATTGA
>g7542.t1 Gene=g7542 Length=198
MQNQSKVLLRKSIKSLVQQITPDNKLRQSNAIMEKLLNMSEYKNSSRISIYLSTENEVNT
IPILTTMFQQNKQVFVPTYAGSEMKMVKVFDMRDYENLPVTKWKIKQPDPDDSSRENPML
TDPLDLILLPGVAFTRNGDRLGHGMGYYDKYLREYFSRHPNVKNHHKTHLIGLAFEEQIV
ESLPTNENDWTLDLILTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g7542.t1 | Gene3D | G3DSA:3.40.50.10420 | - | 1 | 198 | 0 |
| 2 | g7542.t1 | PANTHER | PTHR23407:SF1 | 5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE | 4 | 197 | 0 |
| 3 | g7542.t1 | PANTHER | PTHR23407 | ATPASE INHIBITOR/5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASE | 4 | 197 | 0 |
| 7 | g7542.t1 | PIRSF | PIRSF006806 | 5_FTHF | 1 | 198 | 0 |
| 1 | g7542.t1 | Pfam | PF01812 | 5-formyltetrahydrofolate cyclo-ligase family | 6 | 197 | 0 |
| 4 | g7542.t1 | SUPERFAMILY | SSF100950 | NagB/RpiA/CoA transferase-like | 5 | 197 | 0 |
| 6 | g7542.t1 | TIGRFAM | TIGR02727 | MTHFS_bact: 5-formyltetrahydrofolate cyclo-ligase | 7 | 197 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K01934 (5-formyltetrahydrofolate cyclo-ligase)
Pathway
- This transcript belongs to the following pathways
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.
