Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Ribokinase.

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_1 g13895 g13895.t4 TSS g13895.t4 33189810 33189810
chr_1 g13895 g13895.t4 isoform g13895.t4 33189914 33191195
chr_1 g13895 g13895.t4 exon g13895.t4.exon1 33189914 33189960
chr_1 g13895 g13895.t4 cds g13895.t4.CDS1 33189914 33189960
chr_1 g13895 g13895.t4 exon g13895.t4.exon2 33190015 33190141
chr_1 g13895 g13895.t4 cds g13895.t4.CDS2 33190015 33190141
chr_1 g13895 g13895.t4 exon g13895.t4.exon3 33190558 33190918
chr_1 g13895 g13895.t4 cds g13895.t4.CDS3 33190558 33190918
chr_1 g13895 g13895.t4 exon g13895.t4.exon4 33191002 33191195
chr_1 g13895 g13895.t4 cds g13895.t4.CDS4 33191002 33191195
chr_1 g13895 g13895.t4 TTS g13895.t4 33191390 33191390

Sequences

>g13895.t4 Gene=g13895 Length=729
ATGTTTGATGTTTTAGTTTTTGGGTCATGTATGATTGATTTTATTAGCTATGTTAATCGA
ATGCCAAAATCGGGTGAAACAATTCATTCTCAAGGGTACGAGGTTGGATTTGGTGGCAAA
GGTGCGAATCAGGCAATTGCATCAGCTCGCTTAGGATGTAAAACAGCTATGATTATCCTA
ATTTGCCAATTAGAAATTCCTTTAGACGCAACAATCAAAGCACTGAAAATGTTTAATGGT
CTATCAATTCTTAATGCTGCTCCAGCTCTCGAAAATTTACCCAATATTGCCTACAAATTG
CCAAATATCTTCTGCGTAAATGAACTCGAAGCCGAGGAATTGACAAAAATTACATTCAAT
AAAGTAGAAGACGCCAAGCAAATAATTCAATCTTTGATTCGCGAGAAAGGCTGCAAAATT
GTTATTATGACTCTCGGAAAATATGGTGCCGCACTCAATATCGAAGAGGAATCTGATAAA
AAAATCTATCATGTACCAGTTCCATCTAAAAACAATTTAGTTGTTGACACAACAGGGGCA
GGTGATTGTTTCATAGCTGCATTGGCTTACTTTTACTCAAAATATCCAAAAGCATCACTC
TTACAAAAAGTAGCAGCTTCAATTTCAATTGCGACTCATTCTGTTCAATATAAAGGTACA
CAGTCAAGCTATATCAATTTTCCAAATATCGATCCATTAACTGAAAAGTTTGAGCATCAT
GAACTTTAA

>g13895.t4 Gene=g13895 Length=242
MFDVLVFGSCMIDFISYVNRMPKSGETIHSQGYEVGFGGKGANQAIASARLGCKTAMIIL
ICQLEIPLDATIKALKMFNGLSILNAAPALENLPNIAYKLPNIFCVNELEAEELTKITFN
KVEDAKQIIQSLIREKGCKIVIMTLGKYGAALNIEEESDKKIYHVPVPSKNNLVVDTTGA
GDCFIAALAYFYSKYPKASLLQKVAASISIATHSVQYKGTQSSYINFPNIDPLTEKFEHH
EL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13895.t4 Gene3D G3DSA:3.40.1190.20 - 1 59 7.4E-20
11 g13895.t4 Gene3D G3DSA:3.40.1190.20 - 60 241 2.5E-38
3 g13895.t4 PANTHER PTHR10584:SF166 RIBOKINASE 3 58 1.7E-51
5 g13895.t4 PANTHER PTHR10584 SUGAR KINASE 3 58 1.7E-51
4 g13895.t4 PANTHER PTHR10584:SF166 RIBOKINASE 58 233 1.7E-51
6 g13895.t4 PANTHER PTHR10584 SUGAR KINASE 58 233 1.7E-51
8 g13895.t4 PRINTS PR00990 Ribokinase signature 6 27 6.6E-17
7 g13895.t4 PRINTS PR00990 Ribokinase signature 33 52 6.6E-17
1 g13895.t4 Pfam PF00294 pfkB family carbohydrate kinase 2 59 1.8E-10
2 g13895.t4 Pfam PF00294 pfkB family carbohydrate kinase 82 223 8.9E-22
10 g13895.t4 ProSitePatterns PS00584 pfkB family of carbohydrate kinases signature 2. 176 189 -
9 g13895.t4 SUPERFAMILY SSF53613 Ribokinase-like 1 231 1.36E-42

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:0016301 kinase activity MF
GO:0016773 phosphotransferase activity, alcohol group as acceptor 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