General information for g2508.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Methionyl-tRNA formyltransferase, mitochondrial.
Parent gene
- The parent gene g2508 is located on chr_3: 18335879..18337750 (+ 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_3 | g2508 | g2508.t4 | TSS | g2508.t4 | 18333862 | 18333862 |
| chr_3 | g2508 | g2508.t4 | isoform | g2508.t4 | 18334439 | 18335460 |
| chr_3 | g2508 | g2508.t4 | exon | g2508.t4.exon1 | 18334439 | 18334560 |
| chr_3 | g2508 | g2508.t4 | exon | g2508.t4.exon2 | 18334616 | 18334649 |
| chr_3 | g2508 | g2508.t4 | exon | g2508.t4.exon3 | 18334834 | 18335460 |
| chr_3 | g2508 | g2508.t4 | cds | g2508.t4.CDS1 | 18334836 | 18335459 |
| chr_3 | g2508 | g2508.t4 | TTS | g2508.t4 | 18335491 | 18335491 |
Sequences
>g2508.t4 Gene=g2508 Length=783
ATGATTTTTAGGAATTTTTGTCATAAAATAAAATGGAAATATTTAGAATTATCTCGTAAT
TATTCACATAAAATTTTATTTTTCGGAACAGATAATTTCTCACTTCCATCATTAAAATTA
ATAACTAAACAAAATGATCTATATTCACGTCTTGAGGGATGCTAAATGTACATGCAAGTC
TACTGCCAAAATATCGAGGTGCGAGTCCTATAATTTACGCTATAAAAAATCATGAAACTA
TAACAGGTGTATCAATAATGAAAATCAAGGCAAAAAAGTTTGATGTAGGGGATGTACTTG
CGATGAAAGAAGTATCTATAACAGATGACATTCTTATGTCAGAATTACACGACCAATTAG
CTAATTTAGGAGCACAATTATTAATCGATTGTCTCAAACATTTAGAAGAATGTAAGCCAA
TAAAGCAAGACGAGAGCCAAGCATCATACGCACCTAAAATTGATAAAGAATTTTGCAAAG
TAAGATGGAATGAAATGAGTGCACGTGAGATTTATGATTTATACAGAGCACTCTATTCTT
ACAAGCATGTGTTGACAACATTTAAAAATGAACCGGTTAAGTTGTTAGAATTAAAAAAAT
CTAATGAAGTCATTGAATATAACATTGCTGGACATTTAAAATTTTGTAAAAAAACGAAAA
AACTATTAGTGCATTGTGTTGATGGTGAATGTATAGAAATTAATAAATTACTGATAGCTA
AAAAAGTGATGAGTGCATCAGATTTTAATAATGGATTCTTAAAAAACATAAATGATTTTG
AAA
>g2508.t4 Gene=g2508 Length=208
MLNVHASLLPKYRGASPIIYAIKNHETITGVSIMKIKAKKFDVGDVLAMKEVSITDDILM
SELHDQLANLGAQLLIDCLKHLEECKPIKQDESQASYAPKIDKEFCKVRWNEMSAREIYD
LYRALYSYKHVLTTFKNEPVKLLELKKSNEVIEYNIAGHLKFCKKTKKLLVHCVDGECIE
INKLLIAKKVMSASDFNNGFLKNINDFE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2508.t4 | CDD | cd08704 | Met_tRNA_FMT_C | 104 | 193 | 0 |
| 7 | g2508.t4 | Gene3D | G3DSA:3.40.50.12230 | - | 1 | 203 | 0 |
| 3 | g2508.t4 | PANTHER | PTHR11138 | METHIONYL-TRNA FORMYLTRANSFERASE | 1 | 204 | 0 |
| 4 | g2508.t4 | PANTHER | PTHR11138:SF0 | METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL | 1 | 204 | 0 |
| 1 | g2508.t4 | Pfam | PF00551 | Formyl transferase | 1 | 77 | 0 |
| 2 | g2508.t4 | Pfam | PF02911 | Formyl transferase, C-terminal domain | 100 | 200 | 0 |
| 5 | g2508.t4 | SUPERFAMILY | SSF53328 | Formyltransferase | 1 | 103 | 0 |
| 6 | g2508.t4 | SUPERFAMILY | SSF50486 | FMT C-terminal domain-like | 101 | 200 | 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:0009058 | biosynthetic process | BP |
| GO:0016742 | hydroxymethyl-, formyl- and related transferase activity | MF |
| GO:0003824 | catalytic 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.
