Gene loci information

Transcript annotation

  • This transcript has been annotated as Serine/threonine-protein phosphatase Pgam5, 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_1 g10350 g10350.t4 TTS g10350.t4 9052259 9052259
chr_1 g10350 g10350.t4 isoform g10350.t4 9052507 9053551
chr_1 g10350 g10350.t4 exon g10350.t4.exon1 9052507 9052867
chr_1 g10350 g10350.t4 cds g10350.t4.CDS1 9052574 9052867
chr_1 g10350 g10350.t4 exon g10350.t4.exon2 9052985 9053551
chr_1 g10350 g10350.t4 cds g10350.t4.CDS2 9052985 9053551
chr_1 g10350 g10350.t4 TSS g10350.t4 9053610 9053610

Sequences

>g10350.t4 Gene=g10350 Length=928
ATGTCTTGGAGATATTTTAAGCCATTTTCAAGTGTAAGCTATTATACGATTACTGGTGCT
TCATTATACTTTTTATTAAAAGATGAGAAATTCAAAATTGTTGAAAATTCGAACAAATCT
GAAACAAATAAATTTCCTGAATTTGACTTGAATTGGGATCATAGAGCAGAAACTGCACTC
GTAAAACCATTTAAGGATGGTTCAAATGCTAGCAAGCAAAAGAGTTATAGTGAAAAATTG
GAAAAATATCGCTCGCGAGCTGTTCGGCATATATTACTAATAAGACATGGACAATATTTT
CTTAATGGAACAACAGATAAAGAAAGAGTGCTTACACAATTGGGAAGGGAACAAGCAAAA
ATGACTGGAAATCGTCTAAAAGAATTGGATATTAAGATAACTGAAGCTGTTGTTTCTACT
ATGACACGAGCTAAAGAAACTGCCAATATTTTGCTCAATCAGTTGCCTCAAGCAAAGCAA
TTGGAATTGAAAATTGATTCAATTCTTGAAGAAGGTGCACCCTTAGGTCCTGAACCTAAA
TTTGGTAGTTGGAGGCCCATGGAATATTTCTTTGTAGACGGTGCCCGTATAGAAGCTGCT
TTTAGAAAATATTTTCATCGAGCTGATCCAGAACAAATAAATGATTCTCTTACACTTATT
GTCTGCCATGCAAACGTTATTCGTTATTTCGTTTGTAGAGCACTTCAATGGCCTCCAGAA
GCATGGTTGAGATTTAGTTTACATCATGCTTCAATTACTTGGATATCAATATACCCTAAT
GGAGAAGTTGTTATGAAAATGTATGGCGATGCTGGTCACATGCCTAAGTCACATGTAACA
ACAAGAAATATTGGTGATTAAAAAGTTGTAAAATTTATTTTAATTATTCTTTTGTAATAG
AAAAAAATGAAAGAGTTATTCATAATTT

>g10350.t4 Gene=g10350 Length=286
MSWRYFKPFSSVSYYTITGASLYFLLKDEKFKIVENSNKSETNKFPEFDLNWDHRAETAL
VKPFKDGSNASKQKSYSEKLEKYRSRAVRHILLIRHGQYFLNGTTDKERVLTQLGREQAK
MTGNRLKELDIKITEAVVSTMTRAKETANILLNQLPQAKQLELKIDSILEEGAPLGPEPK
FGSWRPMEYFFVDGARIEAAFRKYFHRADPEQINDSLTLIVCHANVIRYFVCRALQWPPE
AWLRFSLHHASITWISIYPNGEVVMKMYGDAGHMPKSHVTTRNIGD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10350.t4 CDD cd07067 HP_PGM_like 90 264 4.64689E-37
7 g10350.t4 Gene3D G3DSA:3.40.50.1240 - 79 282 8.7E-55
3 g10350.t4 PANTHER PTHR20935 PHOSPHOGLYCERATE MUTASE-RELATED 46 281 2.4E-86
4 g10350.t4 PANTHER PTHR20935:SF0 SERINE/THREONINE-PROTEIN PHOSPHATASE PGAM5, MITOCHONDRIAL 46 281 2.4E-86
2 g10350.t4 Pfam PF00300 Histidine phosphatase superfamily (branch 1) 91 171 6.4E-12
1 g10350.t4 Pfam PF00300 Histidine phosphatase superfamily (branch 1) 195 266 3.4E-9
9 g10350.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
10 g10350.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 26 -
8 g10350.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 27 286 -
6 g10350.t4 SMART SM00855 PGAM_5 90 230 5.2E-11
5 g10350.t4 SUPERFAMILY SSF53254 Phosphoglycerate mutase-like 89 276 4.45E-35

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

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.

Raw TPM values