General information for g10350.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Serine/threonine-protein phosphatase Pgam5, mitochondrial.
Parent gene
- The parent gene g10350 is located on chr_1: 9053551..9057177 (- 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_1 | g10350 | g10350.t1 | TTS | g10350.t1 | 9052259 | 9052259 |
| chr_1 | g10350 | g10350.t1 | isoform | g10350.t1 | 9052574 | 9053551 |
| chr_1 | g10350 | g10350.t1 | exon | g10350.t1.exon1 | 9052574 | 9052870 |
| chr_1 | g10350 | g10350.t1 | cds | g10350.t1.CDS1 | 9052574 | 9052870 |
| chr_1 | g10350 | g10350.t1 | exon | g10350.t1.exon2 | 9052985 | 9053551 |
| chr_1 | g10350 | g10350.t1 | cds | g10350.t1.CDS2 | 9052985 | 9053551 |
| chr_1 | g10350 | g10350.t1 | TSS | g10350.t1 | 9053610 | 9053610 |
Sequences
>g10350.t1 Gene=g10350 Length=864
ATGTCTTGGAGATATTTTAAGCCATTTTCAAGTGTAAGCTATTATACGATTACTGGTGCT
TCATTATACTTTTTATTAAAAGATGAGAAATTCAAAATTGTTGAAAATTCGAACAAATCT
GAAACAAATAAATTTCCTGAATTTGACTTGAATTGGGATCATAGAGCAGAAACTGCACTC
GTAAAACCATTTAAGGATGGTTCAAATGCTAGCAAGCAAAAGAGTTATAGTGAAAAATTG
GAAAAATATCGCTCGCGAGCTGTTCGGCATATATTACTAATAAGACATGGACAATATTTT
CTTAATGGAACAACAGATAAAGAAAGAGTGCTTACACAATTGGGAAGGGAACAAGCAAAA
ATGACTGGAAATCGTCTAAAAGAATTGGATATTAAGATAACTGAAGCTGTTGTTTCTACT
ATGACACGAGCTAAAGAAACTGCCAATATTTTGCTCAATCAGTTGCCTCAAGCAAAGCAA
TTGGAATTGAAAATTGATTCAATTCTTGAAGAAGGTGCACCCTTAGGTCCTGAACCTAAA
TTTGGTAGTTGGAGGCCCATGGAATATCAGTTCTTTGTAGACGGTGCCCGTATAGAAGCT
GCTTTTAGAAAATATTTTCATCGAGCTGATCCAGAACAAATAAATGATTCTCTTACACTT
ATTGTCTGCCATGCAAACGTTATTCGTTATTTCGTTTGTAGAGCACTTCAATGGCCTCCA
GAAGCATGGTTGAGATTTAGTTTACATCATGCTTCAATTACTTGGATATCAATATACCCT
AATGGAGAAGTTGTTATGAAAATGTATGGCGATGCTGGTCACATGCCTAAGTCACATGTA
ACAACAAGAAATATTGGTGATTAA
>g10350.t1 Gene=g10350 Length=287
MSWRYFKPFSSVSYYTITGASLYFLLKDEKFKIVENSNKSETNKFPEFDLNWDHRAETAL
VKPFKDGSNASKQKSYSEKLEKYRSRAVRHILLIRHGQYFLNGTTDKERVLTQLGREQAK
MTGNRLKELDIKITEAVVSTMTRAKETANILLNQLPQAKQLELKIDSILEEGAPLGPEPK
FGSWRPMEYQFFVDGARIEAAFRKYFHRADPEQINDSLTLIVCHANVIRYFVCRALQWPP
EAWLRFSLHHASITWISIYPNGEVVMKMYGDAGHMPKSHVTTRNIGD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10350.t1 | CDD | cd07067 | HP_PGM_like | 90 | 265 | 6.43808E-37 |
| 7 | g10350.t1 | Gene3D | G3DSA:3.40.50.1240 | - | 79 | 283 | 5.1E-56 |
| 3 | g10350.t1 | PANTHER | PTHR20935 | PHOSPHOGLYCERATE MUTASE-RELATED | 46 | 282 | 3.7E-88 |
| 4 | g10350.t1 | PANTHER | PTHR20935:SF0 | SERINE/THREONINE-PROTEIN PHOSPHATASE PGAM5, MITOCHONDRIAL | 46 | 282 | 3.7E-88 |
| 2 | g10350.t1 | Pfam | PF00300 | Histidine phosphatase superfamily (branch 1) | 91 | 171 | 6.0E-12 |
| 1 | g10350.t1 | Pfam | PF00300 | Histidine phosphatase superfamily (branch 1) | 196 | 267 | 4.0E-9 |
| 9 | g10350.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 10 | g10350.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 26 | - |
| 8 | g10350.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 27 | 287 | - |
| 6 | g10350.t1 | SMART | SM00855 | PGAM_5 | 90 | 231 | 5.1E-11 |
| 5 | g10350.t1 | SUPERFAMILY | SSF53254 | Phosphoglycerate mutase-like | 89 | 277 | 1.44E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K15637 (serine/threonine-protein phosphatase PGAM5)
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.
