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.t3 TTS g5772.t3 11842340 11842340
chr_2 g5772 g5772.t3 isoform g5772.t3 11842397 11843753
chr_2 g5772 g5772.t3 exon g5772.t3.exon1 11842397 11842513
chr_2 g5772 g5772.t3 cds g5772.t3.CDS1 11842397 11842513
chr_2 g5772 g5772.t3 exon g5772.t3.exon2 11842576 11843052
chr_2 g5772 g5772.t3 cds g5772.t3.CDS2 11842576 11843052
chr_2 g5772 g5772.t3 exon g5772.t3.exon3 11843109 11843291
chr_2 g5772 g5772.t3 cds g5772.t3.CDS3 11843109 11843291
chr_2 g5772 g5772.t3 exon g5772.t3.exon4 11843457 11843753
chr_2 g5772 g5772.t3 cds g5772.t3.CDS4 11843457 11843747
chr_2 g5772 g5772.t3 TSS g5772.t3 NA NA

Sequences

>g5772.t3 Gene=g5772 Length=1074
GCACAAATGGCAGGAATGAGAGTTGAACCAATTAGAGTTAAAGCAAGTGATGGCACAATT
GATTTGGCTCATTTAAAAGAAAAAGCTGAAGAATTTAGTGAAACTCTTTCATGTCTTATG
ATTACTTATCCATCAACTAATGGAATTTTTGAAGCGGGTGTTGCTGAAGTTTGTGATTTA
ATTCATAAACATGGTGGACAAGTTTATTTAGATGGTGCAAATATGAATGCTCAAGTTGGT
TTATGCAGACCTGGTGATTATGGATCGGACGTTTCACATTTGAATCTTCATAAAACTTTT
GCGTTCTCTATGGCAGGTGGGGGTCCGGGTTGTGGTCCAATTGGTGTTAAAAAACATTTA
GCTCCATTTTTACCATCACATCCAGTCGTAGATGTTTTTCAAGAAAGTGAAGTCAACAAA
AGCTTTGGAACAATTTCAGCAGCACCTTATGGAAGTTCAATGATTTTACCAATTTCTTGG
GCTTATATAAAATTAATGGGAGGAAGAGGTCTTCGCAGAGCAACGCAAGTTGCAATTTTA
AATGCCAATTATATGTCAAAGAAACTCGAGGGTCATTACAAAACACTTTATCGAGATCCA
TCATCAAACTTAGCTGCGCACGAATTTATTCTTGACATTCGTGAATTCAAAAAAACGGCA
AATATTGAAGCAGTTGATATCGCAAAACGTCTAATGGATTATGGTTTTCACGCGCCTACA
ATGTCCTGGCCGGTTGCTGGGACTTTAATGATAGAACCAACAGAATCAGAAGATAAGGAA
GAGCTTGACCGATTTTGTGAAGCTATGATGACAATCCGTGAGGAAATAAGAGACATTGAA
GAGGGCAGAATGGACAAGAAGATTAATCCATTGAAAATGTCTCCACATACACAATTTCAA
GTAGTTAACACTGAATGGAATAGACCATACACAAGAGAGCAAGCAGCTTTTCCTGCACCA
TTTGTGCGTCCTGAAACGAAAGTGTGGCCAACTGTTGCGAGAATAGATGATGCATATGGT
GATAAGCATTTAGTGTGTACATGTCCTCCAATATTACCAGATTTATATACTTAA

>g5772.t3 Gene=g5772 Length=355
MAGMRVEPIRVKASDGTIDLAHLKEKAEEFSETLSCLMITYPSTNGIFEAGVAEVCDLIH
KHGGQVYLDGANMNAQVGLCRPGDYGSDVSHLNLHKTFAFSMAGGGPGCGPIGVKKHLAP
FLPSHPVVDVFQESEVNKSFGTISAAPYGSSMILPISWAYIKLMGGRGLRRATQVAILNA
NYMSKKLEGHYKTLYRDPSSNLAAHEFILDIREFKKTANIEAVDIAKRLMDYGFHAPTMS
WPVAGTLMIEPTESEDKEELDRFCEAMMTIREEIRDIEEGRMDKKINPLKMSPHTQFQVV
NTEWNRPYTREQAAFPAPFVRPETKVWPTVARIDDAYGDKHLVCTCPPILPDLYT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g5772.t3 Gene3D G3DSA:3.40.640.10 - 1 144 0
3 g5772.t3 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase 159 294 0
1 g5772.t3 PANTHER PTHR11773 GLYCINE DEHYDROGENASE, DECARBOXYLATING 1 349 0
2 g5772.t3 SUPERFAMILY SSF53383 PLP-dependent transferases 1 348 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5772/g5772.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5772.t3.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