General information for g2477.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Aminomethyltransferase, mitochondrial.
Parent gene
- The parent gene g2477 is located on chr_3: 18146423..18147736 (- 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 | g2477 | g2477.t1 | TTS | g2477.t1 | 18146298 | 18146298 |
| chr_3 | g2477 | g2477.t1 | isoform | g2477.t1 | 18146423 | 18147736 |
| chr_3 | g2477 | g2477.t1 | exon | g2477.t1.exon1 | 18146423 | 18147418 |
| chr_3 | g2477 | g2477.t1 | cds | g2477.t1.CDS1 | 18146423 | 18147418 |
| chr_3 | g2477 | g2477.t1 | exon | g2477.t1.exon2 | 18147476 | 18147736 |
| chr_3 | g2477 | g2477.t1 | cds | g2477.t1.CDS2 | 18147476 | 18147736 |
| chr_3 | g2477 | g2477.t1 | TSS | g2477.t1 | 18147784 | 18147784 |
Sequences
>g2477.t1 Gene=g2477 Length=1257
ATGAGTTTAATTAAATTTTTCTCTTCGTATTATATAAGAAAAAGTTTGCCAATTAAAAAT
TTGGCATTCTTCTCTACAACGCCATTGCCAGCGCAAGAAGAGCGTGGTGCAAGAAAAACT
TCGCTGTTTGATTTTCATGTCGCGCGTGGAGGAAAAATTGTCAATTTTGCTGGATACTTG
TTGCCTGTTCAATATTCAGATCAAGGAATTGCTACATCACATATTCATACTCGCACACCT
GGATGTGCATCAATATTCGATGTCTCACATATGTTACAAACATATTTAACAGGAAAAGAT
GCAATCGAGTGCTTTGAATCTATCACAACAGCAGATATTCGTGAGCTTAGTGATAGAAAT
GGAACACTAACAGTTTTTACTAACGATAAGGGTGGAATACTCGATGATTTGATTGTCAAT
CGTGTTAATTCCGAATTTCTCTATGTCGTTTCAAATGCGGCACGTAAAGACCACGATAGT
CAATTGATCCGCAACACTGTCGATAACTTTCGTGAGCAGAAAGGCAAAAGTGTGTCTGTA
AGATTTTTTGATACAAAAGAACGTGCACTGCTTGCATTACAAGGACCAGCATCTGCTGCA
GCACTTCAAACATTGACAAAAGTCGACTTGAATCAATTGTATTTCATGACAACGACTGAA
GCTGAAATTGCTGGTGTTAAAGATTGTAGAATCACAAGATGCGGCTATACCGGGGAAGAT
GGTTTTGAAATTTCAATTCTAGGCGATAAAGCATCTTTTATTGCTGAAGCATTGCTTGAT
GTCAAAACAGCAAATGTAAAACTTGCTGGACTTGGAGCTCGAGATTCTTTGAGACTTGAA
GCTGGAATGTGTCTTTATGGTAGTGACATTGACACAACAACAACTCCAATTGAAGCAGGA
TTAGCTTGGTTAGTCGGAAAACGTCGAAGAACAGAAAAGAAATTCCCAGGTGCAGAAATT
ATTATGGATCAACTTAAAAATGGAGTAACTCGTCGTCGAGTTGGAATTAGAATGCTCACA
GGACCACCAGCTCGTCATGGAGTTGGAATATACTCAAATGGTGAAATGATTGGTGAAATT
ACAAGTGGCTGTCCAAGTCCTTCACTCTCTGGAAATGTCGCAATGGGCTACGTCAAAGAG
GAATTCAAGAAATCCGACACGCCTGTAGAGTTGAAAATTCGTGACAAATTCTTTGAAGCA
AAAATTTCAAAAATGCCATTCACCAAATCAAATTATTACCAAAAGACAAAACAATGA
>g2477.t1 Gene=g2477 Length=418
MSLIKFFSSYYIRKSLPIKNLAFFSTTPLPAQEERGARKTSLFDFHVARGGKIVNFAGYL
LPVQYSDQGIATSHIHTRTPGCASIFDVSHMLQTYLTGKDAIECFESITTADIRELSDRN
GTLTVFTNDKGGILDDLIVNRVNSEFLYVVSNAARKDHDSQLIRNTVDNFREQKGKSVSV
RFFDTKERALLALQGPASAAALQTLTKVDLNQLYFMTTTEAEIAGVKDCRITRCGYTGED
GFEISILGDKASFIAEALLDVKTANVKLAGLGARDSLRLEAGMCLYGSDIDTTTTPIEAG
LAWLVGKRRRTEKKFPGAEIIMDQLKNGVTRRRVGIRMLTGPPARHGVGIYSNGEMIGEI
TSGCPSPSLSGNVAMGYVKEEFKKSDTPVELKIRDKFFEAKISKMPFTKSNYYQKTKQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2477.t1 | Gene3D | G3DSA:3.30.1360.120 | Probable tRNA modification gtpase trme; domain 1 | 38 | 281 | 0 |
| 9 | g2477.t1 | Gene3D | G3DSA:3.30.70.1400 | - | 91 | 182 | 0 |
| 8 | g2477.t1 | Gene3D | G3DSA:4.10.1250.10 | Aminomethyltransferase fragment | 282 | 327 | 0 |
| 10 | g2477.t1 | Gene3D | G3DSA:2.40.30.110 | - | 328 | 410 | 0 |
| 3 | g2477.t1 | PANTHER | PTHR43757 | AMINOMETHYLTRANSFERASE | 37 | 415 | 0 |
| 4 | g2477.t1 | PANTHER | PTHR43757:SF2 | AMINOMETHYLTRANSFERASE, MITOCHONDRIAL | 37 | 415 | 0 |
| 12 | g2477.t1 | PIRSF | PIRSF006487 | GCST | 18 | 418 | 0 |
| 2 | g2477.t1 | Pfam | PF01571 | Aminomethyltransferase folate-binding domain | 42 | 303 | 0 |
| 1 | g2477.t1 | Pfam | PF08669 | Glycine cleavage T-protein C-terminal barrel domain | 331 | 407 | 0 |
| 6 | g2477.t1 | SUPERFAMILY | SSF103025 | Folate-binding domain | 35 | 329 | 0 |
| 5 | g2477.t1 | SUPERFAMILY | SSF101790 | Aminomethyltransferase beta-barrel domain | 321 | 414 | 0 |
| 11 | g2477.t1 | TIGRFAM | TIGR00528 | gcvT: glycine cleavage system T protein | 37 | 409 | 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:0006546 | glycine catabolic process | BP |
| GO:0005515 | protein binding | MF |
| GO:0004047 | aminomethyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00605 (aminomethyltransferase)
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.
