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.t28 TTS g6125.t28 14396087 14396087
chr_2 g6125 g6125.t28 isoform g6125.t28 14396643 14397863
chr_2 g6125 g6125.t28 exon g6125.t28.exon1 14396643 14397486
chr_2 g6125 g6125.t28 cds g6125.t28.CDS1 14396644 14397432
chr_2 g6125 g6125.t28 exon g6125.t28.exon2 14397602 14397863
chr_2 g6125 g6125.t28 TSS g6125.t28 14397935 14397935

Sequences

>g6125.t28 Gene=g6125 Length=1106
ATGGCTCTCAACAAATTAAGCATCGAAAACTTGGATTTAGCAGGAAAGCGAGTGTTGATG
CGGTGAGTTTTTAATTTTCCGGTTACAATGGCTGTAAAATAAAATCCTATTTTATTTTTT
TACCAACGAATATGACTAAAATACAATTTACAGCGTTGATTTCAACGTTCCCATTAAAGA
AGGTAAAATTACAAGCAACCAACGTATTGTGGCAGCATTAGAATCTATTAAATATGCATT
GGATAAAGGAGCTAAATCAGTCGTCTTGTGCTCTCACTTGGGACGACCTGATGGCAATAA
AAATCCAAAATACACCATGGCTCCTGTTGCTGATGAGTTGAAAAAATTGTTAGGAAAGGA
TGTCAAATTTATTAATGATTGTGTCGGACCTGAGGTTGAAGCTATTTGTGCAGATCCACC
AACAGGCTCAGTAATTTTGTTGGAAAATCTTCGCTTTTACATTGAAGAAGAGGGAAAAGG
TGTTGATGCAAGTGGTGCTAAAGTGAAGGCAAACGCAGACAAAGTCAAAGAATTCCGTGC
AAGCCTTGCTAAGCTCGGAGACGTCTATATAAATGATGCATTTGGCACAGCTCATCGTGC
TCATTCATCAATGATGGGTGAAGGCTATTCACAACGTGCAGCTGGTTTCTTGATGAACAA
AGAATTGCGTTACTTCTCAAAGGCTCTCGACAACCCAGCACGTCCATTTTTGGCAATTCT
CGGCGGCGCTAAAGTTGCTGACAAAATTCAACTAATTGAGAATTTATTGGATAAAGTTAA
TGAAATGATTATTGGTGGTGGAATGGCATTCACTTTTTTGAAAGTATTGAACAATATGGA
AATTGGTGGCTCATTGTTTGACGAGGAAGGCGCCAAAATTGTACAAAACTTAGTCGAGAA
GGCAAAGAAAAATAATGTGCAGCTTCATTTGCCAGTCGATTTTGTTACTGGTTCAAAGTT
CGGTGAAGACGCTGAAGTTGGCGAAGCATCAGTTGAAAGTGGAATTCCTGCAGGATGGAT
GGGACTTGATGTTGGTCCGAAGACTCGTGAGCTATTTGCTGCTCCAGTCGCTCGTGCAAA
GGTCATCGTTTGGAATGGTCCATGTG

>g6125.t28 Gene=g6125 Length=263
MAPVADELKKLLGKDVKFINDCVGPEVEAICADPPTGSVILLENLRFYIEEEGKGVDASG
AKVKANADKVKEFRASLAKLGDVYINDAFGTAHRAHSSMMGEGYSQRAAGFLMNKELRYF
SKALDNPARPFLAILGGAKVADKIQLIENLLDKVNEMIIGGGMAFTFLKVLNNMEIGGSL
FDEEGAKIVQNLVEKAKKNNVQLHLPVDFVTGSKFGEDAEVGEASVESGIPAGWMGLDVG
PKTRELFAAPVARAKVIVWNGPC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6125.t28 Gene3D G3DSA:3.40.50.1260 - 1 112 0
10 g6125.t28 Gene3D G3DSA:3.40.50.1260 - 119 263 0
2 g6125.t28 PANTHER PTHR11406:SF0 PHOSPHOGLYCERATE KINASE 1 262 0
3 g6125.t28 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE 1 262 0
7 g6125.t28 PRINTS PR00477 Phosphoglycerate kinase family signature 37 52 0
4 g6125.t28 PRINTS PR00477 Phosphoglycerate kinase family signature 80 102 0
6 g6125.t28 PRINTS PR00477 Phosphoglycerate kinase family signature 109 131 0
8 g6125.t28 PRINTS PR00477 Phosphoglycerate kinase family signature 132 151 0
5 g6125.t28 PRINTS PR00477 Phosphoglycerate kinase family signature 256 263 0
1 g6125.t28 Pfam PF00162 Phosphoglycerate kinase 1 262 0
9 g6125.t28 SUPERFAMILY SSF53748 Phosphoglycerate kinase 2 263 0

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