General information for g7440.t2
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.t2 | isoform | g7440.t2 | 23661661 | 23662369 |
| chr_2 | g7440 | g7440.t2 | exon | g7440.t2.exon1 | 23661661 | 23662369 |
| chr_2 | g7440 | g7440.t2 | TTS | g7440.t2 | 23661864 | 23661864 |
| chr_2 | g7440 | g7440.t2 | cds | g7440.t2.CDS1 | 23662006 | 23662368 |
| chr_2 | g7440 | g7440.t2 | TSS | g7440.t2 | 23662705 | 23662705 |
Sequences
>g7440.t2 Gene=g7440 Length=709
TAAAAAGCATGAATGGGTTTCTGTTGATGAATTTAATATCGGAACTGTCGGAATATCAAA
TTACGCACAAGAGGCTTTAGGTGATGTTGTTTATGCTCAATTGCCAGATATTGGAACAAG
TTTTCGACAAAAAGATGAATGTGGTGCATTAGAGAGTGTCAAAGCTGCAAGTGAAATTTA
TTCTCCAGTTAGTGGTGATGTGACAGAAAAAAATGTAGCAGTGGAAGATACACCGAGCCT
TATAAATACATCATGCTATGAGAATGGATGGCTTTTTAAAATTAAACTTGCAAAACCCAG
TGAATTAGATGAACTGTTAGACGAGAAACAATATGAAGAATTTCTTAAGACAGATGCATC
TTAAATCTAGTTTCTAGAAGTATCTACTAGTTATGGTTAATAACAAATGTCGTGATTTTT
AATTTACATACATGTTTTTACACGAGTGATTTTGCATTTCTTCCTCTAATTAATGTTCCT
TTAAAAAATAAAATGTTCAAAAATTTAATTTTCTAATATTTTATATTTAATATTTCAGCA
AATTGATTATCATTGCAATAAAATCTTGAAAATGCCACTCTTAAATTTCATTTTAAAAGT
TTGAAATATTTAACCCTTATAAATTAATAATAACTAACAATACAATTAAAACTTTCAAAA
CATTTTGAAACAAAATGAGCACAATAAAAAGTCAACGATACAATTCAAA
>g7440.t2 Gene=g7440 Length=120
KKHEWVSVDEFNIGTVGISNYAQEALGDVVYAQLPDIGTSFRQKDECGALESVKAASEIY
SPVSGDVTEKNVAVEDTPSLINTSCYENGWLFKIKLAKPSELDELLDEKQYEEFLKTDAS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g7440.t2 | CDD | cd06848 | GCS_H | 1 | 94 | 2.37424E-44 |
| 6 | g7440.t2 | Gene3D | G3DSA:2.40.50.100 | - | 1 | 119 | 8.2E-47 |
| 4 | g7440.t2 | Hamap | MF_00272 | Glycine cleavage system H protein [gcvH]. | 1 | 116 | 32.127708 |
| 2 | g7440.t2 | PANTHER | PTHR11715:SF3 | GLYCINE CLEAVAGE SYSTEM H PROTEIN, MITOCHONDRIAL | 1 | 117 | 9.7E-49 |
| 3 | g7440.t2 | PANTHER | PTHR11715 | GLYCINE CLEAVAGE SYSTEM H PROTEIN | 1 | 117 | 9.7E-49 |
| 1 | g7440.t2 | Pfam | PF01597 | Glycine cleavage H-protein | 1 | 117 | 3.5E-43 |
| 8 | g7440.t2 | ProSitePatterns | PS00189 | 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. | 38 | 67 | - |
| 10 | g7440.t2 | ProSiteProfiles | PS50968 | Biotinyl/lipoyl domain profile. | 13 | 95 | 26.331 |
| 5 | g7440.t2 | SUPERFAMILY | SSF51230 | Single hybrid motif | 1 | 116 | 1.57E-36 |
| 9 | g7440.t2 | TIGRFAM | TIGR00527 | gcvH: glycine cleavage system H protein | 1 | 118 | 2.2E-41 |
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.
