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.t16 TTS g6125.t16 14396087 14396087
chr_2 g6125 g6125.t16 isoform g6125.t16 14396253 14397863
chr_2 g6125 g6125.t16 exon g6125.t16.exon1 14396253 14396278
chr_2 g6125 g6125.t16 cds g6125.t16.CDS1 14396253 14396278
chr_2 g6125 g6125.t16 exon g6125.t16.exon2 14396347 14396506
chr_2 g6125 g6125.t16 cds g6125.t16.CDS2 14396347 14396506
chr_2 g6125 g6125.t16 exon g6125.t16.exon3 14396596 14397434
chr_2 g6125 g6125.t16 cds g6125.t16.CDS3 14396596 14397432
chr_2 g6125 g6125.t16 exon g6125.t16.exon4 14397802 14397863
chr_2 g6125 g6125.t16 TSS g6125.t16 14397935 14397935

Sequences

>g6125.t16 Gene=g6125 Length=1087
ATGGCTCTCAACAAATTAAGCATCGAAAACTTGGATTTAGCAGGAAAGCGAGTGTTGATG
CGCCATGGCTCCTGTTGCTGATGAGTTGAAAAAATTGTTAGGAAAGGATGTCAAATTTAT
TAATGATTGTGTCGGACCTGAGGTTGAAGCTATTTGTGCAGATCCACCAACAGGCTCAGT
AATTTTGTTGGAAAATCTTCGCTTTTACATTGAAGAAGAGGGAAAAGGTGTTGATGCAAG
TGGTGCTAAAGTGAAGGCAAACGCAGACAAAGTCAAAGAATTCCGTGCAAGCCTTGCTAA
GCTCGGAGACGTCTATATAAATGATGCATTTGGCACAGCTCATCGTGCTCATTCATCAAT
GATGGGTGAAGGCTATTCACAACGTGCAGCTGGTTTCTTGATGAACAAAGAATTGCGTTA
CTTCTCAAAGGCTCTCGACAACCCAGCACGTCCATTTTTGGCAATTCTCGGCGGCGCTAA
AGTTGCTGACAAAATTCAACTAATTGAGAATTTATTGGATAAAGTTAATGAAATGATTAT
TGGTGGTGGAATGGCATTCACTTTTTTGAAAGTATTGAACAATATGGAAATTGGTGGCTC
ATTGTTTGACGAGGAAGGCGCCAAAATTGTACAAAACTTAGTCGAGAAGGCAAAGAAAAA
TAATGTGCAGCTTCATTTGCCAGTCGATTTTGTTACTGGTTCAAAGTTCGGTGAAGACGC
TGAAGTTGGCGAAGCATCAGTTGAAAGTGGAATTCCTGCAGGATGGATGGGACTTGATGT
TGGTCCGAAGACTCGTGAGCTATTTGCTGCTCCAGTCGCTCGTGCAAAGGTCATCGTTTG
GAATGGTCCATGTGGTGTTTTTGAATTCCCTAATTTTGCAAAAGGAACAAAAGCTTTGAT
GGATGCTGTTGTAGATGTAACTGCTAAAGGAGCTATTACAATTATTGGTGGAGGTGATAC
AGCAAGTTGCTGTGCAAAGTGGGGAACAGAATCTAAAGTCTCTCATGTTTCAACTGGTGG
TGGTGCAAGTTTGGAATTACTCGAAGGAAAAACTTTACCAGGTGTTGCTGCATTATCAAA
TGCTTAA

>g6125.t16 Gene=g6125 Length=340
MAPVADELKKLLGKDVKFINDCVGPEVEAICADPPTGSVILLENLRFYIEEEGKGVDASG
AKVKANADKVKEFRASLAKLGDVYINDAFGTAHRAHSSMMGEGYSQRAAGFLMNKELRYF
SKALDNPARPFLAILGGAKVADKIQLIENLLDKVNEMIIGGGMAFTFLKVLNNMEIGGSL
FDEEGAKIVQNLVEKAKKNNVQLHLPVDFVTGSKFGEDAEVGEASVESGIPAGWMGLDVG
PKTRELFAAPVARAKVIVWNGPCGVFEFPNFAKGTKALMDAVVDVTAKGAITIIGGGDTA
SCCAKWGTESKVSHVSTGGGASLELLEGKTLPGVAALSNA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g6125.t16 CDD cd00318 Phosphoglycerate_kinase 1 339 0
12 g6125.t16 Gene3D G3DSA:3.40.50.1260 - 2 339 0
13 g6125.t16 Gene3D G3DSA:3.40.50.1260 - 126 315 0
2 g6125.t16 PANTHER PTHR11406:SF10 PHOSPHOGLYCERATE KINASE 2 2 339 0
3 g6125.t16 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE 2 339 0
14 g6125.t16 PIRSF PIRSF000724 Pgk 1 340 0
9 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 37 52 0
5 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 80 102 0
7 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 109 131 0
10 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 132 151 0
4 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 256 281 0
8 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 292 303 0
6 g6125.t16 PRINTS PR00477 Phosphoglycerate kinase family signature 315 332 0
1 g6125.t16 Pfam PF00162 Phosphoglycerate kinase 1 329 0
11 g6125.t16 SUPERFAMILY SSF53748 Phosphoglycerate kinase 2 339 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