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.t20 TTS g6125.t20 14396087 14396087
chr_2 g6125 g6125.t20 isoform g6125.t20 14396253 14397863
chr_2 g6125 g6125.t20 exon g6125.t20.exon1 14396253 14396262
chr_2 g6125 g6125.t20 cds g6125.t20.CDS1 14396255 14396262
chr_2 g6125 g6125.t20 exon g6125.t20.exon2 14396347 14396506
chr_2 g6125 g6125.t20 cds g6125.t20.CDS2 14396347 14396506
chr_2 g6125 g6125.t20 exon g6125.t20.exon3 14396596 14397486
chr_2 g6125 g6125.t20 cds g6125.t20.CDS3 14396596 14397486
chr_2 g6125 g6125.t20 exon g6125.t20.exon4 14397602 14397710
chr_2 g6125 g6125.t20 cds g6125.t20.CDS4 14397602 14397710
chr_2 g6125 g6125.t20 exon g6125.t20.exon5 14397802 14397863
chr_2 g6125 g6125.t20 cds g6125.t20.CDS5 14397802 14397863
chr_2 g6125 g6125.t20 TSS g6125.t20 14397935 14397935

Sequences

>g6125.t20 Gene=g6125 Length=1232
ATGGCTCTCAACAAATTAAGCATCGAAAACTTGGATTTAGCAGGAAAGCGAGTGTTGATG
CGCGTTGATTTCAACGTTCCCATTAAAGAAGGTAAAATTACAAGCAACCAACGTATTGTG
GCAGCATTAGAATCTATTAAATATGCATTGGATAAAGGAGCTAAATCAGTCGTCTTGTGC
TCTCACTTGGGACGACCTGATGGCAATAAAAATCCAAAATACACCATGGCTCCTGTTGCT
GATGAGTTGAAAAAATTGTTAGGAAAGGATGTCAAATTTATTAATGATTGTGTCGGACCT
GAGGTTGAAGCTATTTGTGCAGATCCACCAACAGGCTCAGTAATTTTGTTGGAAAATCTT
CGCTTTTACATTGAAGAAGAGGGAAAAGGTGTTGATGCAAGTGGTGCTAAAGTGAAGGCA
AACGCAGACAAAGTCAAAGAATTCCGTGCAAGCCTTGCTAAGCTCGGAGACGTCTATATA
AATGATGCATTTGGCACAGCTCATCGTGCTCATTCATCAATGATGGGTGAAGGCTATTCA
CAACGTGCAGCTGGTTTCTTGATGAACAAAGAATTGCGTTACTTCTCAAAGGCTCTCGAC
AACCCAGCACGTCCATTTTTGGCAATTCTCGGCGGCGCTAAAGTTGCTGACAAAATTCAA
CTAATTGAGAATTTATTGGATAAAGTTAATGAAATGATTATTGGTGGTGGAATGGCATTC
ACTTTTTTGAAAGTATTGAACAATATGGAAATTGGTGGCTCATTGTTTGACGAGGAAGGC
GCCAAAATTGTACAAAACTTAGTCGAGAAGGCAAAGAAAAATAATGTGCAGCTTCATTTG
CCAGTCGATTTTGTTACTGGTTCAAAGTTCGGTGAAGACGCTGAAGTTGGCGAAGCATCA
GTTGAAAGTGGAATTCCTGCAGGATGGATGGGACTTGATGTTGGTCCGAAGACTCGTGAG
CTATTTGCTGCTCCAGTCGCTCGTGCAAAGGTCATCGTTTGGAATGGTCCATGTGGTGTT
TTTGAATTCCCTAATTTTGCAAAAGGAACAAAAGCTTTGATGGATGCTGTTGTAGATGTA
ACTGCTAAAGGAGCTATTACAATTATTGGTGGAGGTGATACAGCAAGTTGCTGTGCAAAG
TGGGGAACAGAATCTAAAGTCTCTCATGTTTCAACTGGTGGTGGTGCAAGTTTGGAATTA
CTCGAAGGAAAAACTTTACCAGAAATGCTTAA

>g6125.t20 Gene=g6125 Length=410
MALNKLSIENLDLAGKRVLMRVDFNVPIKEGKITSNQRIVAALESIKYALDKGAKSVVLC
SHLGRPDGNKNPKYTMAPVADELKKLLGKDVKFINDCVGPEVEAICADPPTGSVILLENL
RFYIEEEGKGVDASGAKVKANADKVKEFRASLAKLGDVYINDAFGTAHRAHSSMMGEGYS
QRAAGFLMNKELRYFSKALDNPARPFLAILGGAKVADKIQLIENLLDKVNEMIIGGGMAF
TFLKVLNNMEIGGSLFDEEGAKIVQNLVEKAKKNNVQLHLPVDFVTGSKFGEDAEVGEAS
VESGIPAGWMGLDVGPKTRELFAAPVARAKVIVWNGPCGVFEFPNFAKGTKALMDAVVDV
TAKGAITIIGGGDTASCCAKWGTESKVSHVSTGGGASLELLEGKTLPEML

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g6125.t20 CDD cd00318 Phosphoglycerate_kinase 8 407 0.0
15 g6125.t20 Gene3D G3DSA:3.40.50.1260 - 1 71 4.1E-26
16 g6125.t20 Gene3D G3DSA:3.40.50.1260 - 74 408 4.7E-164
17 g6125.t20 Gene3D G3DSA:3.40.50.1260 - 201 390 4.7E-164
4 g6125.t20 Hamap MF_00145 Phosphoglycerate kinase [pgk]. 7 409 35.967541
2 g6125.t20 PANTHER PTHR11406:SF0 PHOSPHOGLYCERATE KINASE 3 408 1.0E-204
3 g6125.t20 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE 3 408 1.0E-204
18 g6125.t20 PIRSF PIRSF000724 Pgk 1 409 6.8E-136
8 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 12 28 1.1E-100
9 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 33 55 1.1E-100
11 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 112 127 1.1E-100
12 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 155 177 1.1E-100
6 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 184 206 1.1E-100
5 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 207 226 1.1E-100
13 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 331 356 1.1E-100
10 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 367 378 1.1E-100
7 g6125.t20 PRINTS PR00477 Phosphoglycerate kinase family signature 390 407 1.1E-100
1 g6125.t20 Pfam PF00162 Phosphoglycerate kinase 8 404 2.4E-150
20 g6125.t20 ProSitePatterns PS00111 Phosphoglycerate kinase signature. 17 27 -
14 g6125.t20 SUPERFAMILY SSF53748 Phosphoglycerate kinase 3 407 8.13E-162

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

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