General information for g13895.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribokinase.
Parent gene
- The parent gene g13895 is located on chr_1: 33191195..33192116 (+ 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_1 | g13895 | g13895.t1 | TSS | g13895.t1 | 33189810 | 33189810 |
| chr_1 | g13895 | g13895.t1 | isoform | g13895.t1 | 33189914 | 33191195 |
| chr_1 | g13895 | g13895.t1 | exon | g13895.t1.exon1 | 33189914 | 33189960 |
| chr_1 | g13895 | g13895.t1 | cds | g13895.t1.CDS1 | 33189914 | 33189960 |
| chr_1 | g13895 | g13895.t1 | exon | g13895.t1.exon2 | 33190015 | 33190366 |
| chr_1 | g13895 | g13895.t1 | cds | g13895.t1.CDS2 | 33190015 | 33190366 |
| chr_1 | g13895 | g13895.t1 | exon | g13895.t1.exon3 | 33190558 | 33190918 |
| chr_1 | g13895 | g13895.t1 | cds | g13895.t1.CDS3 | 33190558 | 33190918 |
| chr_1 | g13895 | g13895.t1 | exon | g13895.t1.exon4 | 33191002 | 33191195 |
| chr_1 | g13895 | g13895.t1 | cds | g13895.t1.CDS4 | 33191002 | 33191195 |
| chr_1 | g13895 | g13895.t1 | TTS | g13895.t1 | 33191390 | 33191390 |
Sequences
>g13895.t1 Gene=g13895 Length=954
ATGTTTGATGTTTTAGTTTTTGGGTCATGTATGATTGATTTTATTAGCTATGTTAATCGA
ATGCCAAAATCGGGTGAAACAATTCATTCTCAAGGGTACGAGGTTGGATTTGGTGGCAAA
GGTGCGAATCAGGCAATTGCATCAGCTCGCTTAGGATGTAAAACAGCTATGATTGGAAAA
ATTGGAAACGACGGTTATGGCAAAAAATATAAAGAACATTTTGAGAAGGAAGGAATAAAC
ACAGATTTCCTTGAATCTGAAGGAGAACATTCCGGTGTTGCATTGATTATTGTGAATTCA
ATAGATGGTAATAATCAGATTGTAATAAATGCCAATGCAAATAAGTACATGAGCGCTGAT
ATTTGTGAAAAAGCAAAAAATATCTTCGAGCAATCAAAGATCCTAATTTGCCAATTAGAA
ATTCCTTTAGACGCAACAATCAAAGCACTGAAAATGTTTAATGGTCTATCAATTCTTAAT
GCTGCTCCAGCTCTCGAAAATTTACCCAATATTGCCTACAAATTGCCAAATATCTTCTGC
GTAAATGAACTCGAAGCCGAGGAATTGACAAAAATTACATTCAATAAAGTAGAAGACGCC
AAGCAAATAATTCAATCTTTGATTCGCGAGAAAGGCTGCAAAATTGTTATTATGACTCTC
GGAAAATATGGTGCCGCACTCAATATCGAAGAGGAATCTGATAAAAAAATCTATCATGTA
CCAGTTCCATCTAAAAACAATTTAGTTGTTGACACAACAGGGGCAGGTGATTGTTTCATA
GCTGCATTGGCTTACTTTTACTCAAAATATCCAAAAGCATCACTCTTACAAAAAGTAGCA
GCTTCAATTTCAATTGCGACTCATTCTGTTCAATATAAAGGTACACAGTCAAGCTATATC
AATTTTCCAAATATCGATCCATTAACTGAAAAGTTTGAGCATCATGAACTTTAA
>g13895.t1 Gene=g13895 Length=317
MFDVLVFGSCMIDFISYVNRMPKSGETIHSQGYEVGFGGKGANQAIASARLGCKTAMIGK
IGNDGYGKKYKEHFEKEGINTDFLESEGEHSGVALIIVNSIDGNNQIVINANANKYMSAD
ICEKAKNIFEQSKILICQLEIPLDATIKALKMFNGLSILNAAPALENLPNIAYKLPNIFC
VNELEAEELTKITFNKVEDAKQIIQSLIREKGCKIVIMTLGKYGAALNIEEESDKKIYHV
PVPSKNNLVVDTTGAGDCFIAALAYFYSKYPKASLLQKVAASISIATHSVQYKGTQSSYI
NFPNIDPLTEKFEHHEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g13895.t1 | CDD | cd01174 | ribokinase | 3 | 299 | 4.3882E-108 |
| 11 | g13895.t1 | Gene3D | G3DSA:3.40.1190.20 | - | 1 | 316 | 2.2E-89 |
| 4 | g13895.t1 | Hamap | MF_01987 | Ribokinase [rbsK]. | 2 | 307 | 23.259758 |
| 2 | g13895.t1 | PANTHER | PTHR10584:SF166 | RIBOKINASE | 3 | 308 | 1.5E-77 |
| 3 | g13895.t1 | PANTHER | PTHR10584 | SUGAR KINASE | 3 | 308 | 1.5E-77 |
| 8 | g13895.t1 | PRINTS | PR00990 | Ribokinase signature | 6 | 27 | 1.1E-27 |
| 6 | g13895.t1 | PRINTS | PR00990 | Ribokinase signature | 33 | 52 | 1.1E-27 |
| 5 | g13895.t1 | PRINTS | PR00990 | Ribokinase signature | 105 | 118 | 1.1E-27 |
| 7 | g13895.t1 | PRINTS | PR00990 | Ribokinase signature | 171 | 186 | 1.1E-27 |
| 9 | g13895.t1 | PRINTS | PR00990 | Ribokinase signature | 216 | 227 | 1.1E-27 |
| 1 | g13895.t1 | Pfam | PF00294 | pfkB family carbohydrate kinase | 2 | 298 | 1.5E-56 |
| 13 | g13895.t1 | ProSitePatterns | PS00583 | pfkB family of carbohydrate kinases signature 1. | 38 | 62 | - |
| 14 | g13895.t1 | ProSitePatterns | PS00584 | pfkB family of carbohydrate kinases signature 2. | 251 | 264 | - |
| 10 | g13895.t1 | SUPERFAMILY | SSF53613 | Ribokinase-like | 1 | 306 | 7.64E-67 |
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 transcript has been annotated with K00852 (ribokinase)
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.
