Gene loci information

Transcript annotation

  • This transcript has been annotated as Phosphoglycerate kinase.

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_2 g6125 g6125.t27 TTS g6125.t27 14396087 14396087
chr_2 g6125 g6125.t27 isoform g6125.t27 14396595 14397863
chr_2 g6125 g6125.t27 exon g6125.t27.exon1 14396595 14397486
chr_2 g6125 g6125.t27 cds g6125.t27.CDS1 14396596 14397486
chr_2 g6125 g6125.t27 exon g6125.t27.exon2 14397602 14397710
chr_2 g6125 g6125.t27 cds g6125.t27.CDS2 14397602 14397710
chr_2 g6125 g6125.t27 exon g6125.t27.exon3 14397802 14397863
chr_2 g6125 g6125.t27 cds g6125.t27.CDS3 14397802 14397863
chr_2 g6125 g6125.t27 TSS g6125.t27 14397935 14397935

Sequences

>g6125.t27 Gene=g6125 Length=1063
ATGGCTCTCAACAAATTAAGCATCGAAAACTTGGATTTAGCAGGAAAGCGAGTGTTGATG
CGCGTTGATTTCAACGTTCCCATTAAAGAAGGTAAAATTACAAGCAACCAACGTATTGTG
GCAGCATTAGAATCTATTAAATATGCATTGGATAAAGGAGCTAAATCAGTCGTCTTGTGC
TCTCACTTGGGACGACCTGATGGCAATAAAAATCCAAAATACACCATGGCTCCTGTTGCT
GATGAGTTGAAAAAATTGTTAGGAAAGGATGTCAAATTTATTAATGATTGTGTCGGACCT
GAGGTTGAAGCTATTTGTGCAGATCCACCAACAGGCTCAGTAATTTTGTTGGAAAATCTT
CGCTTTTACATTGAAGAAGAGGGAAAAGGTGTTGATGCAAGTGGTGCTAAAGTGAAGGCA
AACGCAGACAAAGTCAAAGAATTCCGTGCAAGCCTTGCTAAGCTCGGAGACGTCTATATA
AATGATGCATTTGGCACAGCTCATCGTGCTCATTCATCAATGATGGGTGAAGGCTATTCA
CAACGTGCAGCTGGTTTCTTGATGAACAAAGAATTGCGTTACTTCTCAAAGGCTCTCGAC
AACCCAGCACGTCCATTTTTGGCAATTCTCGGCGGCGCTAAAGTTGCTGACAAAATTCAA
CTAATTGAGAATTTATTGGATAAAGTTAATGAAATGATTATTGGTGGTGGAATGGCATTC
ACTTTTTTGAAAGTATTGAACAATATGGAAATTGGTGGCTCATTGTTTGACGAGGAAGGC
GCCAAAATTGTACAAAACTTAGTCGAGAAGGCAAAGAAAAATAATGTGCAGCTTCATTTG
CCAGTCGATTTTGTTACTGGTTCAAAGTTCGGTGAAGACGCTGAAGTTGGCGAAGCATCA
GTTGAAAGTGGAATTCCTGCAGGATGGATGGGACTTGATGTTGGTCCGAAGACTCGTGAG
CTATTTGCTGCTCCAGTCGCTCGTGCAAAGGTCATCGTTTGGAATGGTCCATGTGGTGTT
TTTGAATTCCCTAATTTTGCAAAAGGAACAAAAGCTTTGATGG

>g6125.t27 Gene=g6125 Length=354
MALNKLSIENLDLAGKRVLMRVDFNVPIKEGKITSNQRIVAALESIKYALDKGAKSVVLC
SHLGRPDGNKNPKYTMAPVADELKKLLGKDVKFINDCVGPEVEAICADPPTGSVILLENL
RFYIEEEGKGVDASGAKVKANADKVKEFRASLAKLGDVYINDAFGTAHRAHSSMMGEGYS
QRAAGFLMNKELRYFSKALDNPARPFLAILGGAKVADKIQLIENLLDKVNEMIIGGGMAF
TFLKVLNNMEIGGSLFDEEGAKIVQNLVEKAKKNNVQLHLPVDFVTGSKFGEDAEVGEAS
VESGIPAGWMGLDVGPKTRELFAAPVARAKVIVWNGPCGVFEFPNFAKGTKALM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6125.t27 CDD cd00318 Phosphoglycerate_kinase 8 354 0.0
12 g6125.t27 Gene3D G3DSA:3.40.50.1260 - 2 187 7.1E-77
13 g6125.t27 Gene3D G3DSA:3.40.50.1260 - 194 354 3.6E-61
2 g6125.t27 PANTHER PTHR11406:SF0 PHOSPHOGLYCERATE KINASE 3 354 4.4E-174
3 g6125.t27 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE 3 354 4.4E-174
14 g6125.t27 PIRSF PIRSF000724 Pgk 1 354 1.9E-113
9 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 12 28 3.5E-80
10 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 33 55 3.5E-80
7 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 112 127 3.5E-80
8 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 155 177 3.5E-80
5 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 184 206 3.5E-80
4 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 207 226 3.5E-80
6 g6125.t27 PRINTS PR00477 Phosphoglycerate kinase family signature 331 354 3.5E-80
1 g6125.t27 Pfam PF00162 Phosphoglycerate kinase 8 353 7.9E-128
16 g6125.t27 ProSitePatterns PS00111 Phosphoglycerate kinase signature. 17 27 -
11 g6125.t27 SUPERFAMILY SSF53748 Phosphoglycerate kinase 3 353 2.71E-136

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:0006096 glycolytic process BP
GO:0004618 phosphoglycerate kinase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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