General information for g12471.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glucosamine-6-phosphate isomerase.
Parent gene
- The parent gene g12471 is located on chr_1: 23921359..23922323 (+ 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 | g12471 | g12471.t4 | TSS | g12471.t4 | 23920175 | 23920175 |
| chr_1 | g12471 | g12471.t4 | isoform | g12471.t4 | 23920282 | 23921904 |
| chr_1 | g12471 | g12471.t4 | exon | g12471.t4.exon1 | 23920282 | 23920287 |
| chr_1 | g12471 | g12471.t4 | exon | g12471.t4.exon2 | 23920678 | 23920913 |
| chr_1 | g12471 | g12471.t4 | cds | g12471.t4.CDS1 | 23920688 | 23920913 |
| chr_1 | g12471 | g12471.t4 | exon | g12471.t4.exon3 | 23920970 | 23921305 |
| chr_1 | g12471 | g12471.t4 | cds | g12471.t4.CDS2 | 23920970 | 23921305 |
| chr_1 | g12471 | g12471.t4 | exon | g12471.t4.exon4 | 23921361 | 23921488 |
| chr_1 | g12471 | g12471.t4 | cds | g12471.t4.CDS3 | 23921361 | 23921488 |
| chr_1 | g12471 | g12471.t4 | exon | g12471.t4.exon5 | 23921548 | 23921625 |
| chr_1 | g12471 | g12471.t4 | cds | g12471.t4.CDS4 | 23921548 | 23921625 |
| chr_1 | g12471 | g12471.t4 | exon | g12471.t4.exon6 | 23921866 | 23921904 |
| chr_1 | g12471 | g12471.t4 | cds | g12471.t4.CDS5 | 23921866 | 23921904 |
| chr_1 | g12471 | g12471.t4 | TTS | g12471.t4 | 23922318 | 23922318 |
Sequences
>g12471.t4 Gene=g12471 Length=823
TTTTTGACGACACAAAATGCGTCTCGTGATTTTGCAAAATAGTGCAACCGTTGGTGAATG
GTCTGCAAAATATGTAATGAAGAGAATCAACGATTTTAAGCCGAGGCCAGAAAAATATTT
TGTCTTGGGCTTACCAACAGGGTCAACTCCACTTGCAATGTATAAAAAACTAATTGAATA
TCATAAAGCTGGACGTATATCATTTAAATATGTTAAAACATTTAATATGGATGAATATGT
TGGTTTGCCTCGAGATCACCCAGAAAGCTATCATTATTATATGTGGAATGAATTTTTCAA
GCACATTGACATTGACCCTGAAAATGTTCATATCCTTGATGGCAATGCATCAGATTTGGT
AGCAGAATGCACAAATTTTGAAGCAAAAATTAAAGAAGCCGGGGGTGTTGAATTGTTCAT
TGGTGGCATTGGACCTGACGGTCACATTGCATTTAATGAGCCAGGTTCATCATTAACAAG
TCGCACACGTGTCAAGACATTAGCACAAGACACATTAGAGGCCAATGCTAGATTCTTTAA
TAATGATATTACAAAAGTTCTGACAAGTGCTTTGACAGTTGGAGTGGGAACAGTTATGGA
TGCAAAGGAAGTCATGATATTGATCACTGGTGCACATAAGAGCTTTGCTTTGTATAAGGC
TATAGAAGAAGGTGTAAATCATATGTGGACTGTTAGTGCTTTTCAACTTCATCCAGCAAC
ACTTTTTATTTGTGATGAAGATGCAACTCTTGAATTAAGAGTCAAGACTGTTAAATATTT
TAAGGCATTGAGTGCCGTTCACAGCAAGATGATCGAGCAATAA
>g12471.t4 Gene=g12471 Length=268
MRLVILQNSATVGEWSAKYVMKRINDFKPRPEKYFVLGLPTGSTPLAMYKKLIEYHKAGR
ISFKYVKTFNMDEYVGLPRDHPESYHYYMWNEFFKHIDIDPENVHILDGNASDLVAECTN
FEAKIKEAGGVELFIGGIGPDGHIAFNEPGSSLTSRTRVKTLAQDTLEANARFFNNDITK
VLTSALTVGVGTVMDAKEVMILITGAHKSFALYKAIEEGVNHMWTVSAFQLHPATLFICD
EDATLELRVKTVKYFKALSAVHSKMIEQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12471.t4 | CDD | cd01399 | GlcN6P_deaminase | 10 | 247 | 1.65612E-137 |
| 6 | g12471.t4 | Gene3D | G3DSA:3.40.50.1360 | - | 1 | 268 | 1.5E-121 |
| 4 | g12471.t4 | Hamap | MF_01241 | Glucosamine-6-phosphate deaminase [nagB]. | 1 | 247 | 38.508579 |
| 2 | g12471.t4 | PANTHER | PTHR11280:SF9 | GLUCOSAMINE-6-PHOSPHATE ISOMERASE 2 | 1 | 267 | 7.2E-151 |
| 3 | g12471.t4 | PANTHER | PTHR11280 | GLUCOSAMINE-6-PHOSPHATE ISOMERASE | 1 | 267 | 7.2E-151 |
| 1 | g12471.t4 | Pfam | PF01182 | Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase | 15 | 229 | 1.1E-18 |
| 8 | g12471.t4 | ProSitePatterns | PS01161 | Glucosamine/galactosamine-6-phosphate isomerases signature. | 125 | 143 | - |
| 5 | g12471.t4 | SUPERFAMILY | SSF100950 | NagB/RpiA/CoA transferase-like | 1 | 261 | 2.09E-100 |
| 9 | g12471.t4 | TIGRFAM | TIGR00502 | nagB: glucosamine-6-phosphate deaminase | 1 | 258 | 1.8E-118 |
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:0004342 | glucosamine-6-phosphate deaminase activity | MF |
| GO:0006044 | N-acetylglucosamine metabolic process | BP |
| GO:0005975 | carbohydrate metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K02564 (glucosamine-6-phosphate deaminase)
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.
