General information for g7440.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Glycine cleavage system H protein, mitochondrial.
Parent gene
- The parent gene g7440 is located on chr_2: 23662006..23662615 (- 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 | g7440 | g7440.t1 | TTS | g7440.t1 | 23661864 | 23661864 |
| chr_2 | g7440 | g7440.t1 | isoform | g7440.t1 | 23662006 | 23662615 |
| chr_2 | g7440 | g7440.t1 | exon | g7440.t1.exon1 | 23662006 | 23662382 |
| chr_2 | g7440 | g7440.t1 | cds | g7440.t1.CDS1 | 23662006 | 23662382 |
| chr_2 | g7440 | g7440.t1 | exon | g7440.t1.exon2 | 23662483 | 23662615 |
| chr_2 | g7440 | g7440.t1 | cds | g7440.t1.CDS2 | 23662483 | 23662615 |
| chr_2 | g7440 | g7440.t1 | TSS | g7440.t1 | 23662705 | 23662705 |
Sequences
>g7440.t1 Gene=g7440 Length=510
ATGGTTTTGTGTCAAATAATTTTTAGAAATTCAACAAATGCACTCAGAAGAATTAATTTA
CCGGCATCAATAAAATCTCAATTTGCACAATCTCATGCAAGGTCATTTAGCACTACTTTA
GTTAACTCTTCAGGGCGAAAATACACTAAAAAGCATGAATGGGTTTCTGTTGATGAATTT
AATATCGGAACTGTCGGAATATCAAATTACGCACAAGAGGCTTTAGGTGATGTTGTTTAT
GCTCAATTGCCAGATATTGGAACAAGTTTTCGACAAAAAGATGAATGTGGTGCATTAGAG
AGTGTCAAAGCTGCAAGTGAAATTTATTCTCCAGTTAGTGGTGATGTGACAGAAAAAAAT
GTAGCAGTGGAAGATACACCGAGCCTTATAAATACATCATGCTATGAGAATGGATGGCTT
TTTAAAATTAAACTTGCAAAACCCAGTGAATTAGATGAACTGTTAGACGAGAAACAATAT
GAAGAATTTCTTAAGACAGATGCATCTTAA
>g7440.t1 Gene=g7440 Length=169
MVLCQIIFRNSTNALRRINLPASIKSQFAQSHARSFSTTLVNSSGRKYTKKHEWVSVDEF
NIGTVGISNYAQEALGDVVYAQLPDIGTSFRQKDECGALESVKAASEIYSPVSGDVTEKN
VAVEDTPSLINTSCYENGWLFKIKLAKPSELDELLDEKQYEEFLKTDAS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7440.t1 | CDD | cd06848 | GCS_H | 48 | 143 | 8.98341E-49 |
| 6 | g7440.t1 | Gene3D | G3DSA:2.40.50.100 | - | 44 | 168 | 3.5E-49 |
| 4 | g7440.t1 | Hamap | MF_00272 | Glycine cleavage system H protein [gcvH]. | 43 | 165 | 34.294609 |
| 2 | g7440.t1 | PANTHER | PTHR11715:SF3 | GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL | 28 | 166 | 5.3E-53 |
| 3 | g7440.t1 | PANTHER | PTHR11715 | GLYCINE CLEAVAGE SYSTEM H PROTEIN | 28 | 166 | 5.3E-53 |
| 1 | g7440.t1 | Pfam | PF01597 | Glycine cleavage H-protein | 46 | 166 | 8.4E-45 |
| 8 | g7440.t1 | ProSitePatterns | PS00189 | 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. | 87 | 116 | - |
| 10 | g7440.t1 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 62 | 144 | 26.331 |
| 5 | g7440.t1 | SUPERFAMILY | SSF51230 | Single hybrid motif | 44 | 165 | 1.44E-38 |
| 9 | g7440.t1 | TIGRFAM | TIGR00527 | gcvH: glycine cleavage system H protein | 47 | 167 | 6.7E-43 |
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:0019464 | glycine decarboxylation via glycine cleavage system | BP |
| GO:0005960 | glycine cleavage complex | CC |
KEGG
Orthology
- This transcript has been annotated with K02437 (glycine cleavage system H protein)
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.
