Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t5 TSS g13895.t5 33189810 33189810
chr_1 g13895 g13895.t5 isoform g13895.t5 33190020 33191195
chr_1 g13895 g13895.t5 exon g13895.t5.exon1 33190020 33190366
chr_1 g13895 g13895.t5 cds g13895.t5.CDS1 33190028 33190366
chr_1 g13895 g13895.t5 exon g13895.t5.exon2 33190558 33190918
chr_1 g13895 g13895.t5 cds g13895.t5.CDS2 33190558 33190918
chr_1 g13895 g13895.t5 exon g13895.t5.exon3 33191002 33191195
chr_1 g13895 g13895.t5 cds g13895.t5.CDS3 33191002 33191195
chr_1 g13895 g13895.t5 TTS g13895.t5 33191390 33191390

Sequences

>g13895.t5 Gene=g13895 Length=902
TTAATCGAATGCCAAAATCGGGTGAAACAATTCATTCTCAAGGGTACGAGGTTGGATTTG
GTGGCAAAGGTGCGAATCAGGCAATTGCATCAGCTCGCTTAGGATGTAAAACAGCTATGA
TTGGAAAAATTGGAAACGACGGTTATGGCAAAAAATATAAAGAACATTTTGAGAAGGAAG
GAATAAACACAGATTTCCTTGAATCTGAAGGAGAACATTCCGGTGTTGCATTGATTATTG
TGAATTCAATAGATGGTAATAATCAGATTGTAATAAATGCCAATGCAAATAAGTACATGA
GCGCTGATATTTGTGAAAAAGCAAAAAATATCTTCGAGCAATCAAAGATCCTAATTTGCC
AATTAGAAATTCCTTTAGACGCAACAATCAAAGCACTGAAAATGTTTAATGGTCTATCAA
TTCTTAATGCTGCTCCAGCTCTCGAAAATTTACCCAATATTGCCTACAAATTGCCAAATA
TCTTCTGCGTAAATGAACTCGAAGCCGAGGAATTGACAAAAATTACATTCAATAAAGTAG
AAGACGCCAAGCAAATAATTCAATCTTTGATTCGCGAGAAAGGCTGCAAAATTGTTATTA
TGACTCTCGGAAAATATGGTGCCGCACTCAATATCGAAGAGGAATCTGATAAAAAAATCT
ATCATGTACCAGTTCCATCTAAAAACAATTTAGTTGTTGACACAACAGGGGCAGGTGATT
GTTTCATAGCTGCATTGGCTTACTTTTACTCAAAATATCCAAAAGCATCACTCTTACAAA
AAGTAGCAGCTTCAATTTCAATTGCGACTCATTCTGTTCAATATAAAGGTACACAGTCAA
GCTATATCAATTTTCCAAATATCGATCCATTAACTGAAAAGTTTGAGCATCATGAACTTT
AA

>g13895.t5 Gene=g13895 Length=297
MPKSGETIHSQGYEVGFGGKGANQAIASARLGCKTAMIGKIGNDGYGKKYKEHFEKEGIN
TDFLESEGEHSGVALIIVNSIDGNNQIVINANANKYMSADICEKAKNIFEQSKILICQLE
IPLDATIKALKMFNGLSILNAAPALENLPNIAYKLPNIFCVNELEAEELTKITFNKVEDA
KQIIQSLIREKGCKIVIMTLGKYGAALNIEEESDKKIYHVPVPSKNNLVVDTTGAGDCFI
AALAYFYSKYPKASLLQKVAASISIATHSVQYKGTQSSYINFPNIDPLTEKFEHHEL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13895.t5 CDD cd01174 ribokinase 1 279 1.2178E-96
10 g13895.t5 Gene3D G3DSA:3.40.1190.20 - 1 296 2.2E-80
4 g13895.t5 Hamap MF_01987 Ribokinase [rbsK]. 1 287 18.808084
2 g13895.t5 PANTHER PTHR10584:SF166 RIBOKINASE 1 288 2.4E-69
3 g13895.t5 PANTHER PTHR10584 SUGAR KINASE 1 288 2.4E-69
8 g13895.t5 PRINTS PR00990 Ribokinase signature 13 32 6.9E-18
5 g13895.t5 PRINTS PR00990 Ribokinase signature 85 98 6.9E-18
6 g13895.t5 PRINTS PR00990 Ribokinase signature 151 166 6.9E-18
7 g13895.t5 PRINTS PR00990 Ribokinase signature 196 207 6.9E-18
1 g13895.t5 Pfam PF00294 pfkB family carbohydrate kinase 5 278 6.7E-51
12 g13895.t5 ProSitePatterns PS00583 pfkB family of carbohydrate kinases signature 1. 18 42 -
13 g13895.t5 ProSitePatterns PS00584 pfkB family of carbohydrate kinases signature 2. 231 244 -
9 g13895.t5 SUPERFAMILY SSF53613 Ribokinase-like 1 286 3.27E-58

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

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