Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Methionyl-tRNA formyltransferase, mitochondrial.

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_3 g2508 g2508.t3 TSS g2508.t3 18333862 18333862
chr_3 g2508 g2508.t3 isoform g2508.t3 18334439 18335460
chr_3 g2508 g2508.t3 exon g2508.t3.exon1 18334439 18334560
chr_3 g2508 g2508.t3 cds g2508.t3.CDS1 18334439 18334560
chr_3 g2508 g2508.t3 exon g2508.t3.exon2 18334616 18334773
chr_3 g2508 g2508.t3 cds g2508.t3.CDS2 18334616 18334773
chr_3 g2508 g2508.t3 exon g2508.t3.exon3 18334834 18335460
chr_3 g2508 g2508.t3 cds g2508.t3.CDS3 18334834 18335459
chr_3 g2508 g2508.t3 TTS g2508.t3 18335491 18335491

Sequences

>g2508.t3 Gene=g2508 Length=907
ATGATTTTTAGGAATTTTTGTCATAAAATAAAATGGAAATATTTAGAATTATCTCGTAAT
TATTCACATAAAATTTTATTTTTCGGAACAGATAATTTCTCACTTCCATCATTAAAATTA
ATAACTAAACAAAATGATCTATATTCACGTCTTGAGGTTGTCACTTCTTTTAAATCAAAG
AAAAATCCAATAAAAGACTTTGCTAACGAACAAAAATTACCTGTGCATGATTGGGAAAGT
CTTAAAAACGATTTAAAAATATTTAGTGAATTTGACATAGGGATGCTAAATGTACATGCA
AGTCTACTGCCAAAATATCGAGGTGCGAGTCCTATAATTTACGCTATAAAAAATCATGAA
ACTATAACAGGTGTATCAATAATGAAAATCAAGGCAAAAAAGTTTGATGTAGGGGATGTA
CTTGCGATGAAAGAAGTATCTATAACAGATGACATTCTTATGTCAGAATTACACGACCAA
TTAGCTAATTTAGGAGCACAATTATTAATCGATTGTCTCAAACATTTAGAAGAATGTAAG
CCAATAAAGCAAGACGAGAGCCAAGCATCATACGCACCTAAAATTGATAAAGAATTTTGC
AAAGTAAGATGGAATGAAATGAGTGCACGTGAGATTTATGATTTATACAGAGCACTCTAT
TCTTACAAGCATGTGTTGACAACATTTAAAAATGAACCGGTTAAGTTGTTAGAATTAAAA
AAATCTAATGAAGTCATTGAATATAACATTGCTGGACATTTAAAATTTTGTAAAAAAACG
AAAAAACTATTAGTGCATTGTGTTGATGGTGAATGTATAGAAATTAATAAATTACTGATA
GCTAAAAAAGTGATGAGTGCATCAGATTTTAATAATGGATTCTTAAAAAACATAAATGAT
TTTGAAA

>g2508.t3 Gene=g2508 Length=302
MIFRNFCHKIKWKYLELSRNYSHKILFFGTDNFSLPSLKLITKQNDLYSRLEVVTSFKSK
KNPIKDFANEQKLPVHDWESLKNDLKIFSEFDIGMLNVHASLLPKYRGASPIIYAIKNHE
TITGVSIMKIKAKKFDVGDVLAMKEVSITDDILMSELHDQLANLGAQLLIDCLKHLEECK
PIKQDESQASYAPKIDKEFCKVRWNEMSAREIYDLYRALYSYKHVLTTFKNEPVKLLELK
KSNEVIEYNIAGHLKFCKKTKKLLVHCVDGECIEINKLLIAKKVMSASDFNNGFLKNIND
FE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2508.t3 CDD cd08646 FMT_core_Met-tRNA-FMT_N 24 195 0e+00
10 g2508.t3 CDD cd08704 Met_tRNA_FMT_C 198 287 0e+00
8 g2508.t3 Gene3D G3DSA:3.40.50.170 Formyltransferase 23 86 1e-07
7 g2508.t3 Gene3D G3DSA:3.40.50.170 Formyltransferase 87 196 0e+00
9 g2508.t3 Gene3D G3DSA:3.10.25.10 - 197 301 0e+00
3 g2508.t3 PANTHER PTHR11138 METHIONYL-TRNA FORMYLTRANSFERASE 18 298 0e+00
4 g2508.t3 PANTHER PTHR11138:SF0 METHIONYL-TRNA FORMYLTRANSFERASE, MITOCHONDRIAL 18 298 0e+00
1 g2508.t3 Pfam PF00551 Formyl transferase 89 171 0e+00
2 g2508.t3 Pfam PF02911 Formyl transferase, C-terminal domain 194 294 0e+00
5 g2508.t3 SUPERFAMILY SSF53328 Formyltransferase 24 197 0e+00
6 g2508.t3 SUPERFAMILY SSF50486 FMT C-terminal domain-like 195 294 0e+00

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.

Raw TPM values