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.t12 TTS g6125.t12 14396087 14396087
chr_2 g6125 g6125.t12 isoform g6125.t12 14396253 14397228
chr_2 g6125 g6125.t12 exon g6125.t12.exon1 14396253 14396303
chr_2 g6125 g6125.t12 cds g6125.t12.CDS1 14396281 14396303
chr_2 g6125 g6125.t12 exon g6125.t12.exon2 14396386 14396506
chr_2 g6125 g6125.t12 cds g6125.t12.CDS2 14396386 14396506
chr_2 g6125 g6125.t12 exon g6125.t12.exon3 14396596 14397228
chr_2 g6125 g6125.t12 cds g6125.t12.CDS3 14396596 14397138
chr_2 g6125 g6125.t12 TSS g6125.t12 14397935 14397935

Sequences

>g6125.t12 Gene=g6125 Length=805
AAAGTCAAAGAATTCCGTGCAAGCCTTGCTAAGCTCGGAGACGTCTATATAAATGATGCA
TTTGGCACAGCTCATCGTGCTCATTCATCAATGATGGGTGAAGGCTATTCACAACGTGCA
GCTGGTTTCTTGATGAACAAAGAATTGCGTTACTTCTCAAAGGCTCTCGACAACCCAGCA
CGTCCATTTTTGGCAATTCTCGGCGGCGCTAAAGTTGCTGACAAAATTCAACTAATTGAG
AATTTATTGGATAAAGTTAATGAAATGATTATTGGTGGTGGAATGGCATTCACTTTTTTG
AAAGTATTGAACAATATGGAAATTGGTGGCTCATTGTTTGACGAGGAAGGCGCCAAAATT
GTACAAAACTTAGTCGAGAAGGCAAAGAAAAATAATGTGCAGCTTCATTTGCCAGTCGAT
TTTGTTACTGGTTCAAAGTTCGGTGAAGACGCTGAAGTTGGCGAAGCATCAGTTGAAAGT
GGAATTCCTGCAGGATGGATGGGACTTGATGTTGGTCCGAAGACTCGTGAGCTATTTGCT
GCTCCAGTCGCTCGTGCAAAGGTCATCGTTTGGAATGGTCCATGTGGTGTTTTTGAATTC
CCTAATTTTGCAAAAGGAACAAAAGCTTTGATGGATGCTGTTGTAGATGTAACTGCTAAA
GGAGCTATTACAATTATTGGTGGAGGTGATACAGCAAGTTGCTGTGCAAAGTGGGGAACA
GAATCTAAAGTCTCTCATGTTTCAACTGGTGGTGTCAATTTTTCTATTCTTTATTAAAGG
TGTTGCTGCATTATCAAATGCTTAA

>g6125.t12 Gene=g6125 Length=228
MMGEGYSQRAAGFLMNKELRYFSKALDNPARPFLAILGGAKVADKIQLIENLLDKVNEMI
IGGGMAFTFLKVLNNMEIGGSLFDEEGAKIVQNLVEKAKKNNVQLHLPVDFVTGSKFGED
AEVGEASVESGIPAGWMGLDVGPKTRELFAAPVARAKVIVWNGPCGVFEFPNFAKGTKAL
MDAVVDVTAKGAITIIGGGDTASCCAKWGTESKVSHVSTGGVNFSILY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g6125.t12 Gene3D G3DSA:3.40.50.1260 - 1 221 0
10 g6125.t12 Gene3D G3DSA:3.40.50.1260 - 28 217 0
2 g6125.t12 PANTHER PTHR11406:SF10 PHOSPHOGLYCERATE KINASE 2 1 222 0
3 g6125.t12 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE 1 222 0
4 g6125.t12 PRINTS PR00477 Phosphoglycerate kinase family signature 11 33 0
6 g6125.t12 PRINTS PR00477 Phosphoglycerate kinase family signature 34 53 0
8 g6125.t12 PRINTS PR00477 Phosphoglycerate kinase family signature 158 183 0
7 g6125.t12 PRINTS PR00477 Phosphoglycerate kinase family signature 194 205 0
5 g6125.t12 PRINTS PR00477 Phosphoglycerate kinase family signature 217 228 0
1 g6125.t12 Pfam PF00162 Phosphoglycerate kinase 8 222 0
9 g6125.t12 SUPERFAMILY SSF53748 Phosphoglycerate kinase 3 221 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