General information for g5443.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycerate kinase.
Parent gene
- The parent gene g5443 is located on chr_2: 9619222..9620912 (- 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 | g5443 | g5443.t1 | TTS | g5443.t1 | 9618935 | 9618935 |
| chr_2 | g5443 | g5443.t1 | isoform | g5443.t1 | 9619222 | 9620912 |
| chr_2 | g5443 | g5443.t1 | exon | g5443.t1.exon1 | 9619222 | 9620495 |
| chr_2 | g5443 | g5443.t1 | cds | g5443.t1.CDS1 | 9619222 | 9620495 |
| chr_2 | g5443 | g5443.t1 | exon | g5443.t1.exon2 | 9620554 | 9620625 |
| chr_2 | g5443 | g5443.t1 | cds | g5443.t1.CDS2 | 9620554 | 9620625 |
| chr_2 | g5443 | g5443.t1 | exon | g5443.t1.exon3 | 9620735 | 9620912 |
| chr_2 | g5443 | g5443.t1 | cds | g5443.t1.CDS3 | 9620735 | 9620912 |
| chr_2 | g5443 | g5443.t1 | TSS | g5443.t1 | 9620984 | 9620984 |
Sequences
>g5443.t1 Gene=g5443 Length=1524
ATGGAGAATATAATAAAGGATATTTTCTATGCAGCTGTAGAGTCTGTTAAACCAAGTGAA
TTAATTACAAAAAATAAATTTTTATCACTTAAAAATATTGAAAATAGAGAGATTATTGAA
TTAAATCAAAATAATGAATCATATCAACTGGATGCAACTAATAAAAGACTTCATATAGTT
GGTTTCGGTAAAGCCTCACTACCTCTTGCAATAGAGCTAGAATCGATTTTGAAAGAACGA
ATCACGGGTGGAATTTTGAGTGTACCAGTTAATGCTACGAAATATCATTCATTATCAAAA
AATTCGAAATTGCATGTGTTTGAAGGAGCTGCTGGTAATTTACCTGATTATGATTCAATG
CGTAATGCAGAGAAAATTAAAAATTATATTTTGAATTTAAATAATGATGATATTTTATTT
TGTCTAATAACCGGTGGAGGTTCAGCTTTACTAAGTTTGCCAATAGAACCAATTACGCTT
GATGAAAAAACAGCTTTAATTAAACAACTATCAAGAGCAGGTGCATCAATAAATGAACTT
AATACTGTAAGAATAGCAATATCGCAAGTCAAAGGAGGAAAACTTGCACTAATGGCTAAG
AATGTACATAAAATAATTTCATTAATCATCAGTGATATCATAAATGATCCATTAGAGTTA
ATTGCTAGTGGACCAACTATTCCATATAAAATACCATCAACAGATGAGTTATCGCCATTG
CAAGTCCTTGAAAAATATATAGGTGACCGAATGGAAAATACATTATCACCTTCGATATTG
AACACAATAAAAAATATGAACGAAAAAAATCAAGATTCTCAGATGGTGATAAAAAATTCC
CAAACCTTTCTACTTGGCAATAATCGGAATGCTATAGATGCTGCTATGAATCAAGCAAAA
ATTCATAACTTTGTACCTGTATATCTATCTGCTTCAGTTCAAGGCAATGTTAATGAAATC
AGTGTGGCTTTTTTCGAACTTGCTTGTGCCATTCAATCGTATTCATCTGCTTCAACTTGT
ATCGAGTTTGCAAATTCGCTTAAATGTATTTTGGAGAAACTTAATGCACAAACAAACTTT
GTTGCAGATTTGATTGAAGCACTTAATCAAAAATCATCCGATGGAATATGTATTGTTAGT
AGTGGTGAAACTGTAGTAAAAGTCAATTGTAATGAAGGTATTGGTGGTCGATCTCAAGAA
CTTTGTTTGCGTTTTACAAAACTTTGCTATGACGCAGGATTGTCGCTTGACAACTTGTTG
TTTCTTTCTGCTGGTACAGATGGCATTGATGGCAACAACGATGCTGCAGGTGCTATTGGT
GGAACAAGAATTCTTCGTGATATTAAAGAAAATGTAGCGTGTGTGATGAGTGATTATATT
TATAGAAATGACTCATATCGATTTTATAAGAATTTTATTGGAAAATATTCTGGTGATGGC
TATCATATTCACACAGGAATCACAGGTACTAACGTTATGGATATACATTTGTTGATGATA
ATGCCAAAAGTAAAATTATCATGA
>g5443.t1 Gene=g5443 Length=507
MENIIKDIFYAAVESVKPSELITKNKFLSLKNIENREIIELNQNNESYQLDATNKRLHIV
GFGKASLPLAIELESILKERITGGILSVPVNATKYHSLSKNSKLHVFEGAAGNLPDYDSM
RNAEKIKNYILNLNNDDILFCLITGGGSALLSLPIEPITLDEKTALIKQLSRAGASINEL
NTVRIAISQVKGGKLALMAKNVHKIISLIISDIINDPLELIASGPTIPYKIPSTDELSPL
QVLEKYIGDRMENTLSPSILNTIKNMNEKNQDSQMVIKNSQTFLLGNNRNAIDAAMNQAK
IHNFVPVYLSASVQGNVNEISVAFFELACAIQSYSSASTCIEFANSLKCILEKLNAQTNF
VADLIEALNQKSSDGICIVSSGETVVKVNCNEGIGGRSQELCLRFTKLCYDAGLSLDNLL
FLSAGTDGIDGNNDAAGAIGGTRILRDIKENVACVMSDYIYRNDSYRFYKNFIGKYSGDG
YHIHTGITGTNVMDIHLLMIMPKVKLS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5443.t1 | Coils | Coil | Coil | 31 | 51 | - |
| 6 | g5443.t1 | Coils | Coil | Coil | 351 | 371 | - |
| 3 | g5443.t1 | PANTHER | PTHR12227 | GLYCERATE KINASE | 3 | 501 | 1.1E-125 |
| 1 | g5443.t1 | Pfam | PF13660 | Domain of unknown function (DUF4147) | 6 | 247 | 1.1E-63 |
| 2 | g5443.t1 | Pfam | PF05161 | MOFRL family | 376 | 494 | 1.2E-25 |
| 4 | g5443.t1 | SUPERFAMILY | SSF82544 | GckA/TtuD-like | 3 | 500 | 2.88E-91 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5443/g5443.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5443.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0008887 | glycerate kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K11529 (glycerate 2-kinase)
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.
