General information for g3910.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative N-acylneuraminate-9-phosphatase.
Parent gene
- The parent gene g3910 is located on chr_3: 28792848..28794920 (+ 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_3 | g3910 | g3910.t1 | isoform | g3910.t1 | 28792848 | 28794920 |
| chr_3 | g3910 | g3910.t1 | exon | g3910.t1.exon1 | 28792848 | 28793312 |
| chr_3 | g3910 | g3910.t1 | cds | g3910.t1.CDS1 | 28792848 | 28793312 |
| chr_3 | g3910 | g3910.t1 | exon | g3910.t1.exon2 | 28794501 | 28794920 |
| chr_3 | g3910 | g3910.t1 | cds | g3910.t1.CDS2 | 28794501 | 28794920 |
| chr_3 | g3910 | g3910.t1 | TTS | g3910.t1 | 28795149 | 28795149 |
| chr_3 | g3910 | g3910.t1 | TSS | g3910.t1 | NA | NA |
Sequences
>g3910.t1 Gene=g3910 Length=885
ATGGATAAAGAAGAGGCTGATATGTGCACAGCGAGCTACTTGAAAGAATTCAGAAAGTGT
CCTGACCATATTTCAATGTCACTCGATCAATGGCGTTCAGAATTATGGAACAATGCTTTA
CCACCGAAGTACAAGCACTTATCTTACGAAATCTATCAACAATGGTTGCAGTATCGTTAT
CACTACTTAGAGCTTCCAACGGAACTTGTACAGATGCTGAGACAACTTCGTAAAAATTAT
CTTCTTGTCATCATCACAAATGGACCAAGCAATGCTCAGTGGGAGAAAATTCATAAATTA
GGTTTCAATATGGGCAAAAATTCTCTATTTGATTGTATACTTGTTTCAGCTGATTGTGGT
TTTGAAAAGCCTGATAGAAGAATTTTTGAAACTGCTTGCAATTATTTAGGCATATTACCA
CAAAATTGCATTATGGTCGGTGATAAACTGGAGAGTGATATAAAGGGAGGTAAACTGGCG
AATTTGTTAGCTACGGTATGGATACCATTGAATTTTCCAGCGACAGTTGAGCCAAATGGT
AGTATTGTTCCCGATATAACACTAAGTAGCATCTATGAGTTGAAATCGCTACTAATTGTC
GATGACCAGCCACAGCAGCAATTAACTGGAGGAAATGCGAGATCACTAAAGCTAAAAGCA
TCACGTTCCATTATGAGTAATGGACCATTAAGTTTGTCATCGTCTACATCATCATCATCT
TCATCCCCATCATCAACAAATTCCGCTCCCTTTGCTAGCACCGGATGTTTTTCATCGTCA
TCCTCCAAGGCAAAGAACATCACACCATATCCAAGACGCTTCCTTTCACCACCGATACCG
ATTGATTTAGATAATGATGCGTCGAATCAATCCGATGGCTCATGA
>g3910.t1 Gene=g3910 Length=294
MDKEEADMCTASYLKEFRKCPDHISMSLDQWRSELWNNALPPKYKHLSYEIYQQWLQYRY
HYLELPTELVQMLRQLRKNYLLVIITNGPSNAQWEKIHKLGFNMGKNSLFDCILVSADCG
FEKPDRRIFETACNYLGILPQNCIMVGDKLESDIKGGKLANLLATVWIPLNFPATVEPNG
SIVPDITLSSIYELKSLLIVDDQPQQQLTGGNARSLKLKASRSIMSNGPLSLSSSTSSSS
SSPSSTNSAPFASTGCFSSSSSKAKNITPYPRRFLSPPIPIDLDNDASNQSDGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g3910.t1 | Gene3D | G3DSA:1.20.120.710 | - | 12 | 63 | 1.2E-45 |
| 6 | g3910.t1 | Gene3D | G3DSA:3.40.50.1000 | - | 64 | 195 | 1.2E-45 |
| 4 | g3910.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 267 | - |
| 5 | g3910.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 227 | 294 | - |
| 2 | g3910.t1 | PANTHER | PTHR46470 | N-ACYLNEURAMINATE-9-PHOSPHATASE | 3 | 199 | 2.2E-53 |
| 1 | g3910.t1 | Pfam | PF13419 | Haloacid dehalogenase-like hydrolase | 38 | 162 | 2.2E-18 |
| 3 | g3910.t1 | SUPERFAMILY | SSF56784 | HAD-like | 11 | 198 | 5.91E-31 |
| 8 | g3910.t1 | TIGRFAM | TIGR01549 | HAD-SF-IA-v1: HAD hydrolase, family IA, variant 1 | 66 | 160 | 5.7E-12 |
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:0016787 | hydrolase activity | 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.
