Gene loci information

Transcript annotation

  • This transcript has been annotated as Aminomethyltransferase, 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 g2477 g2477.t4 TTS g2477.t4 18146298 18146298
chr_3 g2477 g2477.t4 isoform g2477.t4 18146423 18147736
chr_3 g2477 g2477.t4 exon g2477.t4.exon1 18146423 18146821
chr_3 g2477 g2477.t4 cds g2477.t4.CDS1 18146817 18146821
chr_3 g2477 g2477.t4 exon g2477.t4.exon2 18146926 18147418
chr_3 g2477 g2477.t4 cds g2477.t4.CDS2 18146926 18147418
chr_3 g2477 g2477.t4 exon g2477.t4.exon3 18147476 18147736
chr_3 g2477 g2477.t4 cds g2477.t4.CDS3 18147476 18147736
chr_3 g2477 g2477.t4 TSS g2477.t4 18147784 18147784

Sequences

>g2477.t4 Gene=g2477 Length=1153
ATGAGTTTAATTAAATTTTTCTCTTCGTATTATATAAGAAAAAGTTTGCCAATTAAAAAT
TTGGCATTCTTCTCTACAACGCCATTGCCAGCGCAAGAAGAGCGTGGTGCAAGAAAAACT
TCGCTGTTTGATTTTCATGTCGCGCGTGGAGGAAAAATTGTCAATTTTGCTGGATACTTG
TTGCCTGTTCAATATTCAGATCAAGGAATTGCTACATCACATATTCATACTCGCACACCT
GGATGTGCATCAATATTCGATGTCTCACATATGTTACAAACATATTTAACAGGAAAAGAT
GCAATCGAGTGCTTTGAATCTATCACAACAGCAGATATTCGTGAGCTTAGTGATAGAAAT
GGAACACTAACAGTTTTTACTAACGATAAGGGTGGAATACTCGATGATTTGATTGTCAAT
CGTGTTAATTCCGAATTTCTCTATGTCGTTTCAAATGCGGCACGTAAAGACCACGATAGT
CAATTGATCCGCAACACTGTCGATAACTTTCGTGAGCAGAAAGGCAAAAGTGTGTCTGTA
AGATTTTTTGATACAAAAGAACGTGCACTGCTTGCATTACAAGGACCAGCATCTGCTGCA
GCACTTCAAACATTGACAAAAGTCGACTTGAATCAATTGTATTTCATGACAACGACTGAA
GCTGAAATTGCTGGTGTTAAAGATTGTAGAATCACAAGATGCGGCTATACCGGGGAAGAT
GGTTTTGAAATTTCAATTCTAGGCGATAAAGCATGGTAGTGACATTGACACAACAACAAC
TCCAATTGAAGCAGGATTAGCTTGGTTAGTCGGAAAACGTCGAAGAACAGAAAAGAAATT
CCCAGGTGCAGAAATTATTATGGATCAACTTAAAAATGGAGTAACTCGTCGTCGAGTTGG
AATTAGAATGCTCACAGGACCACCAGCTCGTCATGGAGTTGGAATATACTCAAATGGTGA
AATGATTGGTGAAATTACAAGTGGCTGTCCAAGTCCTTCACTCTCTGGAAATGTCGCAAT
GGGCTACGTCAAAGAGGAATTCAAGAAATCCGACACGCCTGTAGAGTTGAAAATTCGTGA
CAAATTCTTTGAAGCAAAAATTTCAAAAATGCCATTCACCAAATCAAATTATTACCAAAA
GACAAAACAATGA

>g2477.t4 Gene=g2477 Length=252
MSLIKFFSSYYIRKSLPIKNLAFFSTTPLPAQEERGARKTSLFDFHVARGGKIVNFAGYL
LPVQYSDQGIATSHIHTRTPGCASIFDVSHMLQTYLTGKDAIECFESITTADIRELSDRN
GTLTVFTNDKGGILDDLIVNRVNSEFLYVVSNAARKDHDSQLIRNTVDNFREQKGKSVSV
RFFDTKERALLALQGPASAAALQTLTKVDLNQLYFMTTTEAEIAGVKDCRITRCGYTGED
GFEISILGDKAW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g2477.t4 Gene3D G3DSA:3.30.1360.120 Probable tRNA modification gtpase trme; domain 1 38 250 0
6 g2477.t4 Gene3D G3DSA:3.30.70.1400 - 91 182 0
2 g2477.t4 PANTHER PTHR43757 AMINOMETHYLTRANSFERASE 37 246 0
3 g2477.t4 PANTHER PTHR43757:SF2 AMINOMETHYLTRANSFERASE, MITOCHONDRIAL 37 246 0
7 g2477.t4 PIRSF PIRSF006487 GCST 18 252 0
1 g2477.t4 Pfam PF01571 Aminomethyltransferase folate-binding domain 42 249 0
4 g2477.t4 SUPERFAMILY SSF103025 Folate-binding domain 35 246 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:0005515 protein binding 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