General information for g5772.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycine dehydrogenase (decarboxylating), mitochondrial.
Parent gene
- The parent gene g5772 is located on chr_2: 11844985..11846408 (- 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_2 | g5772 | g5772.t1 | TTS | g5772.t1 | 11842340 | 11842340 |
| chr_2 | g5772 | g5772.t1 | isoform | g5772.t1 | 11842397 | 11846408 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon1 | 11842397 | 11842513 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS1 | 11842397 | 11842513 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon2 | 11842576 | 11843052 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS2 | 11842576 | 11843052 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon3 | 11843109 | 11843272 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS3 | 11843109 | 11843272 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon4 | 11843379 | 11843397 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS4 | 11843379 | 11843397 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon5 | 11843457 | 11844729 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS5 | 11843457 | 11844729 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon6 | 11844790 | 11844923 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS6 | 11844790 | 11844923 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon7 | 11844985 | 11845247 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS7 | 11844985 | 11845247 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon8 | 11845301 | 11845428 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS8 | 11845301 | 11845428 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon9 | 11845485 | 11845532 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS9 | 11845485 | 11845532 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon10 | 11845591 | 11845678 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS10 | 11845591 | 11845678 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon11 | 11846087 | 11846165 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS11 | 11846087 | 11846165 |
| chr_2 | g5772 | g5772.t1 | exon | g5772.t1.exon12 | 11846217 | 11846408 |
| chr_2 | g5772 | g5772.t1 | cds | g5772.t1.CDS12 | 11846217 | 11846408 |
| chr_2 | g5772 | g5772.t1 | TSS | g5772.t1 | 11846482 | 11846482 |
Sequences
>g5772.t1 Gene=g5772 Length=2982
ATGCAAAGAAATTTAGCAAAATGTTTAGTACAAAGATGCAATGGTGTGATAAATAAAAAA
GTTTATTTAACATCAGTGCGATCACTTGCAACAGTTAAGGAAATTTTTCAAAATAAAAGT
GAATTTCCTACTCGACACATTGGTCCAAGAAAGACTGATGTTGTGTCGATGCTAGATTTA
TTAGGATTTAAAACACTTGATGAGCTTACTGACAAAGTTCTGCCACAAGACATCAAATTC
AATCGTGATTTAGATATCGATCTACCATTAAATGAACATGAACTGATTAATAGAATACGG
GCTGTTGCAAAGAAGAATGAAATATGGCGATCGTATATCGGCATGGGATATCATAATTGT
TATGTTCCTCATCCAATATTGAGAAATATTTTTGAAAATCCAGGATGGACAACACAATAT
ACACCATATCAACCAGAAATTGCACAAGGACGATTGGAATCATTACTGAACTATCAAACA
CTTGTTACTGAAATGACTGGTTTAGATGTTGCAAATGCAAGTTTATTAGATGAAGGAACT
GCCGCTGCTGAAGCAATGAGTCTTTGTTATCGTCATAATAAGCGTAAAAAAATTTATCTT
TCACAAAATCTTCATCCGCAAACATTGTCAGTTGTCGAAACTCGTTTGAAAGCTTTAGAT
GTTGAAGTTATTATTGGTCCAATATCAGAAGCTAATTTCACAAATCATGAATATTCTGGA
ATGTTATTACAATATCCCGACACATATGGAAATGTTGTTGATTTTGAATCAATTGCTGCA
GAAGCTAAGAAAAATGGAACGTTGGTTTGTGTAGCAACAGATTTGTTAGCTTTAACACTA
TTGCGACCACCAGCAGAATTTGGTGCAGATATTGCAGTCGGAACATCGCAACGTTTGGGT
GTACCATTGGGCTATGGTGGACCACATGCTGGATTTTTCGCTTGCAAACAGAATTTCGTT
CGACTCATTCCTGGTAGAATGGTAGGTGTTACGCGCGACCAAGACGGCCACGATGCATAT
CGACTCGCACTGCAGACACGTGAACAGCATATAAGACGTGATAAGGCAACCAGTAATATT
TGCACGGCTCAAGCATTATTGGCTAATATGAGTGCAATGTTCGCTATATATCACGGACCA
GAAGGCTTAAAAGAGATTGCCAGCAATATTCACAATGGTGCGATAACACTTAGCTATGGC
ATTAAGCGTGCTGGACATCAACAGCTCAATGAACACTTTTTCGATACGATACATGTAATT
CCAAATGGATTAACAATTGACGAGATTAAAGAACGCGCTGAAAGAAAGAAAATTAATTTG
CGGTATCTTGATGATGGATCAGTAACAATTGCGCTAGACGAGACAGTAAAGACTGAAGAT
TTGGACGATTTGCTGTGGATTTTCAAGGCAGACACACTCAGTGAAATATTAAAAGACCCA
AATGCTCTGTTTGAAAACATTACTTATACACAATTCAAACGAACTTCGTCTTTTTTGACC
CATCCAATTTTTAGTAAATTTCATAGCGAATCAAGAATGGTACGATACATGAAGCAGCTT
GAAAACAAAGATATTTCTCTTGTTCATTCAATGATTCCGCTTGGGTCATGTACAATGAAA
TTAAACTCGACGACAGAAATGATTCCATGCTCATTTCGACATTTTACTGAAATTCATCCA
TTTGCACCTGTCGAACAAGCTAAAGGTTATCATCAAATGTTTGATGAATTGGAAAAGGAT
CTCTGTGAAATTACTGGTTATGATAAAATTTCATTTCAACCTAACAGTGGAGCACAAGGA
GAATATGCTGGATTGCGAGCAATTCGAGGTTACCATGAAGCTAATGGCCAACATCAAAGA
AATGTTTGCTTGATTCCAGTGTCAGCACATGGCACAAATCCTGCAAGTGCACAAATGGCA
GGAATGAGAGTTGAACCAATTAGAGTTAAAGCAAGTGATGGCACAATTGATTTGGCTCAT
TTAAAAGAAAAAGCTGAAGAATTTAGTGAAACTCTTTCATGTCTTATGATTACTTATCCA
TCAACTAATGGAATTTTTGAAGCGGGTGTTGCTGAAGTTTGTGATTTAATTCATAAACAT
GGTGGACAAGTTTATTTAGATGGTGCAAATATGAATGCTCAAGTTGGTTTATGCAGACCT
GGTGATTATGGATCGGACGTTTCACATTTGAATCTTCATAAAACTTTCTGCATTCCTCAT
GGAGGTGGGGGTCCGGGTTGTGGTCCAATTGGTGTTAAAAAACATTTAGCTCCATTTTTA
CCATCACATCCAGTCGTAGATGTTTTTCAAGAAAGTGAAGTCAACAAAAGCTTTGGAACA
ATTTCAGCAGCACCTTATGGAAGTTCAATGATTTTACCAATTTCTTGGGCTTATATAAAA
TTAATGGGAGGAAGAGGTCTTCGCAGAGCAACGCAAGTTGCAATTTTAAATGCCAATTAT
ATGTCAAAGAAACTCGAGGGTCATTACAAAACACTTTATCGAGATCCATCATCAAACTTA
GCTGCGCACGAATTTATTCTTGACATTCGTGAATTCAAAAAAACGGCAAATATTGAAGCA
GTTGATATCGCAAAACGTCTAATGGATTATGGTTTTCACGCGCCTACAATGTCCTGGCCG
GTTGCTGGGACTTTAATGATAGAACCAACAGAATCAGAAGATAAGGAAGAGCTTGACCGA
TTTTGTGAAGCTATGATGACAATCCGTGAGGAAATAAGAGACATTGAAGAGGGCAGAATG
GACAAGAAGATTAATCCATTGAAAATGTCTCCACATACACAATTTCAAGTAGTTAACACT
GAATGGAATAGACCATACACAAGAGAGCAAGCAGCTTTTCCTGCACCATTTGTGCGTCCT
GAAACGAAAGTGTGGCCAACTGTTGCGAGAATAGATGATGCATATGGTGATAAGCATTTA
GTGTGTACATGTCCTCCAATATTACCAGATTTATATACTTAA
>g5772.t1 Gene=g5772 Length=993
MQRNLAKCLVQRCNGVINKKVYLTSVRSLATVKEIFQNKSEFPTRHIGPRKTDVVSMLDL
LGFKTLDELTDKVLPQDIKFNRDLDIDLPLNEHELINRIRAVAKKNEIWRSYIGMGYHNC
YVPHPILRNIFENPGWTTQYTPYQPEIAQGRLESLLNYQTLVTEMTGLDVANASLLDEGT
AAAEAMSLCYRHNKRKKIYLSQNLHPQTLSVVETRLKALDVEVIIGPISEANFTNHEYSG
MLLQYPDTYGNVVDFESIAAEAKKNGTLVCVATDLLALTLLRPPAEFGADIAVGTSQRLG
VPLGYGGPHAGFFACKQNFVRLIPGRMVGVTRDQDGHDAYRLALQTREQHIRRDKATSNI
CTAQALLANMSAMFAIYHGPEGLKEIASNIHNGAITLSYGIKRAGHQQLNEHFFDTIHVI
PNGLTIDEIKERAERKKINLRYLDDGSVTIALDETVKTEDLDDLLWIFKADTLSEILKDP
NALFENITYTQFKRTSSFLTHPIFSKFHSESRMVRYMKQLENKDISLVHSMIPLGSCTMK
LNSTTEMIPCSFRHFTEIHPFAPVEQAKGYHQMFDELEKDLCEITGYDKISFQPNSGAQG
EYAGLRAIRGYHEANGQHQRNVCLIPVSAHGTNPASAQMAGMRVEPIRVKASDGTIDLAH
LKEKAEEFSETLSCLMITYPSTNGIFEAGVAEVCDLIHKHGGQVYLDGANMNAQVGLCRP
GDYGSDVSHLNLHKTFCIPHGGGGPGCGPIGVKKHLAPFLPSHPVVDVFQESEVNKSFGT
ISAAPYGSSMILPISWAYIKLMGGRGLRRATQVAILNANYMSKKLEGHYKTLYRDPSSNL
AAHEFILDIREFKKTANIEAVDIAKRLMDYGFHAPTMSWPVAGTLMIEPTESEDKEELDR
FCEAMMTIREEIRDIEEGRMDKKINPLKMSPHTQFQVVNTEWNRPYTREQAAFPAPFVRP
ETKVWPTVARIDDAYGDKHLVCTCPPILPDLYT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5772.t1 | CDD | cd00613 | GDC-P | 92 | 468 | 4.28932E-154 |
| 14 | g5772.t1 | CDD | cd00613 | GDC-P | 510 | 905 | 3.05247E-141 |
| 9 | g5772.t1 | Gene3D | G3DSA:3.40.640.10 | - | 125 | 381 | 4.8E-107 |
| 8 | g5772.t1 | Gene3D | G3DSA:3.40.640.10 | - | 548 | 782 | 9.6E-63 |
| 7 | g5772.t1 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase | 797 | 929 | 3.9E-42 |
| 3 | g5772.t1 | PANTHER | PTHR11773:SF1 | GLYCINE DEHYDROGENASE (DECARBOXYLATING), MITOCHONDRIAL | 39 | 987 | 0.0 |
| 4 | g5772.t1 | PANTHER | PTHR11773 | GLYCINE DEHYDROGENASE, DECARBOXYLATING | 39 | 987 | 0.0 |
| 1 | g5772.t1 | Pfam | PF02347 | Glycine cleavage system P-protein | 45 | 468 | 4.2E-182 |
| 2 | g5772.t1 | Pfam | PF02347 | Glycine cleavage system P-protein | 502 | 762 | 9.0E-7 |
| 12 | g5772.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 777 | - |
| 13 | g5772.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 778 | 799 | - |
| 11 | g5772.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 800 | 993 | - |
| 6 | g5772.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 45 | 467 | 1.47E-91 |
| 5 | g5772.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 508 | 986 | 4.83E-96 |
| 10 | g5772.t1 | TIGRFAM | TIGR00461 | gcvP: glycine dehydrogenase | 45 | 984 | 0.0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5772/g5772.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5772.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006546 | glycine catabolic process | BP |
| GO:0006544 | glycine metabolic process | BP |
| GO:0003824 | catalytic activity | MF |
| GO:0055114 | NA | NA |
| GO:0004375 | glycine dehydrogenase (decarboxylating) activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00281 (glycine dehydrogenase)
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.
