General information for g6125.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Phosphoglycerate kinase.
Parent gene
- The parent gene g6125 is located on chr_2: 14396643..14397863 (- strand)
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.t17 | TTS | g6125.t17 | 14396087 | 14396087 |
| chr_2 | g6125 | g6125.t17 | isoform | g6125.t17 | 14396253 | 14397863 |
| chr_2 | g6125 | g6125.t17 | exon | g6125.t17.exon1 | 14396253 | 14396278 |
| chr_2 | g6125 | g6125.t17 | cds | g6125.t17.CDS1 | 14396253 | 14396278 |
| chr_2 | g6125 | g6125.t17 | exon | g6125.t17.exon2 | 14396347 | 14396506 |
| chr_2 | g6125 | g6125.t17 | cds | g6125.t17.CDS2 | 14396347 | 14396506 |
| chr_2 | g6125 | g6125.t17 | exon | g6125.t17.exon3 | 14396596 | 14397486 |
| chr_2 | g6125 | g6125.t17 | cds | g6125.t17.CDS3 | 14396596 | 14397432 |
| chr_2 | g6125 | g6125.t17 | exon | g6125.t17.exon4 | 14397602 | 14397710 |
| chr_2 | g6125 | g6125.t17 | exon | g6125.t17.exon5 | 14397813 | 14397863 |
| chr_2 | g6125 | g6125.t17 | TSS | g6125.t17 | 14397935 | 14397935 |
Sequences
>g6125.t17 Gene=g6125 Length=1237
ATGGCTCTCAACAAATTAAGCATCGAAAACTTGGATTTAGCAGGAAAGCGACGTTGATTT
CAACGTTCCCATTAAAGAAGGTAAAATTACAAGCAACCAACGTATTGTGGCAGCATTAGA
ATCTATTAAATATGCATTGGATAAAGGAGCTAAATCAGTCGTCTTGTGCTCTCACTTGGG
ACGACCTGATGGCAATAAAAATCCAAAATACACCATGGCTCCTGTTGCTGATGAGTTGAA
AAAATTGTTAGGAAAGGATGTCAAATTTATTAATGATTGTGTCGGACCTGAGGTTGAAGC
TATTTGTGCAGATCCACCAACAGGCTCAGTAATTTTGTTGGAAAATCTTCGCTTTTACAT
TGAAGAAGAGGGAAAAGGTGTTGATGCAAGTGGTGCTAAAGTGAAGGCAAACGCAGACAA
AGTCAAAGAATTCCGTGCAAGCCTTGCTAAGCTCGGAGACGTCTATATAAATGATGCATT
TGGCACAGCTCATCGTGCTCATTCATCAATGATGGGTGAAGGCTATTCACAACGTGCAGC
TGGTTTCTTGATGAACAAAGAATTGCGTTACTTCTCAAAGGCTCTCGACAACCCAGCACG
TCCATTTTTGGCAATTCTCGGCGGCGCTAAAGTTGCTGACAAAATTCAACTAATTGAGAA
TTTATTGGATAAAGTTAATGAAATGATTATTGGTGGTGGAATGGCATTCACTTTTTTGAA
AGTATTGAACAATATGGAAATTGGTGGCTCATTGTTTGACGAGGAAGGCGCCAAAATTGT
ACAAAACTTAGTCGAGAAGGCAAAGAAAAATAATGTGCAGCTTCATTTGCCAGTCGATTT
TGTTACTGGTTCAAAGTTCGGTGAAGACGCTGAAGTTGGCGAAGCATCAGTTGAAAGTGG
AATTCCTGCAGGATGGATGGGACTTGATGTTGGTCCGAAGACTCGTGAGCTATTTGCTGC
TCCAGTCGCTCGTGCAAAGGTCATCGTTTGGAATGGTCCATGTGGTGTTTTTGAATTCCC
TAATTTTGCAAAAGGAACAAAAGCTTTGATGGATGCTGTTGTAGATGTAACTGCTAAAGG
AGCTATTACAATTATTGGTGGAGGTGATACAGCAAGTTGCTGTGCAAAGTGGGGAACAGA
ATCTAAAGTCTCTCATGTTTCAACTGGTGGTGGTGCAAGTTTGGAATTACTCGAAGGAAA
AACTTTACCAGGTGTTGCTGCATTATCAAATGCTTAA
>g6125.t17 Gene=g6125 Length=340
MAPVADELKKLLGKDVKFINDCVGPEVEAICADPPTGSVILLENLRFYIEEEGKGVDASG
AKVKANADKVKEFRASLAKLGDVYINDAFGTAHRAHSSMMGEGYSQRAAGFLMNKELRYF
SKALDNPARPFLAILGGAKVADKIQLIENLLDKVNEMIIGGGMAFTFLKVLNNMEIGGSL
FDEEGAKIVQNLVEKAKKNNVQLHLPVDFVTGSKFGEDAEVGEASVESGIPAGWMGLDVG
PKTRELFAAPVARAKVIVWNGPCGVFEFPNFAKGTKALMDAVVDVTAKGAITIIGGGDTA
SCCAKWGTESKVSHVSTGGGASLELLEGKTLPGVAALSNA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g6125.t17 | CDD | cd00318 | Phosphoglycerate_kinase | 1 | 339 | 0 |
| 12 | g6125.t17 | Gene3D | G3DSA:3.40.50.1260 | - | 2 | 339 | 0 |
| 13 | g6125.t17 | Gene3D | G3DSA:3.40.50.1260 | - | 126 | 315 | 0 |
| 2 | g6125.t17 | PANTHER | PTHR11406:SF10 | PHOSPHOGLYCERATE KINASE 2 | 2 | 339 | 0 |
| 3 | g6125.t17 | PANTHER | PTHR11406 | PHOSPHOGLYCERATE KINASE | 2 | 339 | 0 |
| 14 | g6125.t17 | PIRSF | PIRSF000724 | Pgk | 1 | 340 | 0 |
| 9 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 37 | 52 | 0 |
| 5 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 80 | 102 | 0 |
| 7 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 109 | 131 | 0 |
| 10 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 132 | 151 | 0 |
| 4 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 256 | 281 | 0 |
| 8 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 292 | 303 | 0 |
| 6 | g6125.t17 | PRINTS | PR00477 | Phosphoglycerate kinase family signature | 315 | 332 | 0 |
| 1 | g6125.t17 | Pfam | PF00162 | Phosphoglycerate kinase | 1 | 329 | 0 |
| 11 | g6125.t17 | 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.
