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.t2 TSS g13895.t2 33189810 33189810
chr_1 g13895 g13895.t2 isoform g13895.t2 33189914 33190904
chr_1 g13895 g13895.t2 exon g13895.t2.exon1 33189914 33189960
chr_1 g13895 g13895.t2 cds g13895.t2.CDS1 33189914 33189960
chr_1 g13895 g13895.t2 exon g13895.t2.exon2 33190015 33190366
chr_1 g13895 g13895.t2 cds g13895.t2.CDS2 33190015 33190366
chr_1 g13895 g13895.t2 exon g13895.t2.exon3 33190558 33190904
chr_1 g13895 g13895.t2 cds g13895.t2.CDS3 33190558 33190902
chr_1 g13895 g13895.t2 TTS g13895.t2 33191390 33191390

Sequences

>g13895.t2 Gene=g13895 Length=746
ATGTTTGATGTTTTAGTTTTTGGGTCATGTATGATTGATTTTATTAGCTATGTTAATCGA
ATGCCAAAATCGGGTGAAACAATTCATTCTCAAGGGTACGAGGTTGGATTTGGTGGCAAA
GGTGCGAATCAGGCAATTGCATCAGCTCGCTTAGGATGTAAAACAGCTATGATTGGAAAA
ATTGGAAACGACGGTTATGGCAAAAAATATAAAGAACATTTTGAGAAGGAAGGAATAAAC
ACAGATTTCCTTGAATCTGAAGGAGAACATTCCGGTGTTGCATTGATTATTGTGAATTCA
ATAGATGGTAATAATCAGATTGTAATAAATGCCAATGCAAATAAGTACATGAGCGCTGAT
ATTTGTGAAAAAGCAAAAAATATCTTCGAGCAATCAAAGATCCTAATTTGCCAATTAGAA
ATTCCTTTAGACGCAACAATCAAAGCACTGAAAATGTTTAATGGTCTATCAATTCTTAAT
GCTGCTCCAGCTCTCGAAAATTTACCCAATATTGCCTACAAATTGCCAAATATCTTCTGC
GTAAATGAACTCGAAGCCGAGGAATTGACAAAAATTACATTCAATAAAGTAGAAGACGCC
AAGCAAATAATTCAATCTTTGATTCGCGAGAAAGGCTGCAAAATTGTTATTATGACTCTC
GGAAAATATGGTGCCGCACTCAATATCGAAGAGGAATCTGATAAAAAAATCTATCATGTA
CCAGTTCCATCTAAAAACAATTTAGT

>g13895.t2 Gene=g13895 Length=248
MFDVLVFGSCMIDFISYVNRMPKSGETIHSQGYEVGFGGKGANQAIASARLGCKTAMIGK
IGNDGYGKKYKEHFEKEGINTDFLESEGEHSGVALIIVNSIDGNNQIVINANANKYMSAD
ICEKAKNIFEQSKILICQLEIPLDATIKALKMFNGLSILNAAPALENLPNIAYKLPNIFC
VNELEAEELTKITFNKVEDAKQIIQSLIREKGCKIVIMTLGKYGAALNIEEESDKKIYHV
PVPSKNNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13895.t2 CDD cd01174 ribokinase 3 241 1.96211E-90
11 g13895.t2 Gene3D G3DSA:3.40.1190.20 - 1 246 1.1E-70
2 g13895.t2 PANTHER PTHR10584:SF166 RIBOKINASE 3 242 3.4E-62
3 g13895.t2 PANTHER PTHR10584 SUGAR KINASE 3 242 3.4E-62
7 g13895.t2 PRINTS PR00990 Ribokinase signature 6 27 4.3E-28
5 g13895.t2 PRINTS PR00990 Ribokinase signature 33 52 4.3E-28
4 g13895.t2 PRINTS PR00990 Ribokinase signature 105 118 4.3E-28
6 g13895.t2 PRINTS PR00990 Ribokinase signature 171 186 4.3E-28
8 g13895.t2 PRINTS PR00990 Ribokinase signature 216 227 4.3E-28
1 g13895.t2 Pfam PF00294 pfkB family carbohydrate kinase 2 244 5.7E-44
10 g13895.t2 ProSitePatterns PS00583 pfkB family of carbohydrate kinases signature 1. 38 62 -
9 g13895.t2 SUPERFAMILY SSF53613 Ribokinase-like 1 243 1.54E-51

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
GO:0004747 ribokinase activity MF
GO:0006014 D-ribose metabolic process BP

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