Gene loci information

Transcript annotation

  • This transcript has been annotated as Glycine dehydrogenase (decarboxylating), 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_2 g5772 g5772.t6 isoform g5772.t6 11844985 11846408
chr_2 g5772 g5772.t6 exon g5772.t6.exon1 11844985 11845247
chr_2 g5772 g5772.t6 cds g5772.t6.CDS1 11844985 11845247
chr_2 g5772 g5772.t6 exon g5772.t6.exon2 11845301 11845428
chr_2 g5772 g5772.t6 cds g5772.t6.CDS2 11845301 11845428
chr_2 g5772 g5772.t6 exon g5772.t6.exon3 11845485 11845532
chr_2 g5772 g5772.t6 cds g5772.t6.CDS3 11845485 11845532
chr_2 g5772 g5772.t6 exon g5772.t6.exon4 11845591 11845678
chr_2 g5772 g5772.t6 cds g5772.t6.CDS4 11845591 11845678
chr_2 g5772 g5772.t6 exon g5772.t6.exon5 11846087 11846165
chr_2 g5772 g5772.t6 cds g5772.t6.CDS5 11846087 11846165
chr_2 g5772 g5772.t6 exon g5772.t6.exon6 11846217 11846408
chr_2 g5772 g5772.t6 cds g5772.t6.CDS6 11846217 11846408
chr_2 g5772 g5772.t6 TSS g5772.t6 11846482 11846482
chr_2 g5772 g5772.t6 TTS g5772.t6 NA NA

Sequences

>g5772.t6 Gene=g5772 Length=798
ATGCAAAGAAATTTAGCAAAATGTTTAGTACAAAGATGCAATGGTGTGATAAATAAAAAA
GTTTATTTAACATCAGTGCGATCACTTGCAACAGTTAAGGAAATTTTTCAAAATAAAAGT
GAATTTCCTACTCGACACATTGGTCCAAGAAAGACTGATGTTGTGTCGATGCTAGATTTA
TTAGGATTTAAAACACTTGATGAGCTTACTGACAAAGTTCTGCCACAAGACATCAAATTC
AATCGTGATTTAGATATCGATCTACCATTAAATGAACATGAACTGATTAATAGAATACGG
GCTGTTGCAAAGAAGAATGAAATATGGCGATCGTATATCGGCATGGGATATCATAATTGT
TATGTTCCTCATCCAATATTGAGAAATATTTTTGAAAATCCAGGATGGACAACACAATAT
ACACCATATCAACCAGAAATTGCACAAGGACGATTGGAATCATTACTGAACTATCAAACA
CTTGTTACTGAAATGACTGGTTTAGATGTTGCAAATGCAAGTTTATTAGATGAAGGAACT
GCCGCTGCTGAAGCAATGAGTCTTTGTTATCGTCATAATAAGCGTAAAAAAATTTATCTT
TCACAAAATCTTCATCCGCAAACATTGTCAGTTGTCGAAACTCGTTTGAAAGCTTTAGAT
GTTGAAGTTATTATTGGTCCAATATCAGAAGCTAATTTCACAAATCATGAATATTCTGGA
ATGTTATTACAATATCCCGACACATATGGAAATGTTGTTGATTTTGAATCAATTGCTGCA
GAAGCTAAGAAAAATGGA

>g5772.t6 Gene=g5772 Length=266
MQRNLAKCLVQRCNGVINKKVYLTSVRSLATVKEIFQNKSEFPTRHIGPRKTDVVSMLDL
LGFKTLDELTDKVLPQDIKFNRDLDIDLPLNEHELINRIRAVAKKNEIWRSYIGMGYHNC
YVPHPILRNIFENPGWTTQYTPYQPEIAQGRLESLLNYQTLVTEMTGLDVANASLLDEGT
AAAEAMSLCYRHNKRKKIYLSQNLHPQTLSVVETRLKALDVEVIIGPISEANFTNHEYSG
MLLQYPDTYGNVVDFESIAAEAKKNG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g5772.t6 Gene3D G3DSA:3.40.640.10 - 125 266 0
2 g5772.t6 PANTHER PTHR11773:SF7 GLYCINE DEHYDROGENASE (DECARBOXYLATING) 36 264 0
3 g5772.t6 PANTHER PTHR11773 GLYCINE DEHYDROGENASE, DECARBOXYLATING 36 264 0
1 g5772.t6 Pfam PF02347 Glycine cleavage system P-protein 45 265 0
4 g5772.t6 SUPERFAMILY SSF53383 PLP-dependent transferases 45 266 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5772/g5772.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5772.t6.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006546 glycine catabolic process BP
GO:0003824 catalytic activity MF
GO:0055114 NA NA
GO:0004375 glycine dehydrogenase (decarboxylating) 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. There were no conditions that were differentially expressed