General information for g5260.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Alpha-N-acetylgalactosaminidase.
Parent gene
- The parent gene g5260 is located on chr_2: 8286298..8288636 (- 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_2 | g5260 | g5260.t2 | isoform | g5260.t2 | 8286298 | 8286787 |
| chr_2 | g5260 | g5260.t2 | exon | g5260.t2.exon1 | 8286298 | 8286787 |
| chr_2 | g5260 | g5260.t2 | cds | g5260.t2.CDS1 | 8286298 | 8286786 |
| chr_2 | g5260 | g5260.t2 | TSS | g5260.t2 | NA | NA |
| chr_2 | g5260 | g5260.t2 | TTS | g5260.t2 | NA | NA |
Sequences
>g5260.t2 Gene=g5260 Length=490
GAATGATCCAGACACTCTTCTACTTGGAAATTTTGGCCTAAGTTACGAACAAAGTAAAGC
ACAATTGGCAATTTGGGCAGTTATTGCTGCTCCATTTCTCTTATCAAATGATCTTAGGAC
TGTCACACCGGAAATTAAAGAACTTTTACTTAATCGAGAAATTATCGCAGTTGACCAAGA
TCCACTTGGTATTCAAGGTAAACAACTAAAGAAGGGTAATGGAATTGAAGTATGGGTGAG
ACCAATAACACCAATTGTCGGAAATGAATACTCGTATGCTGTTGCATTTGTTTCAAGACG
TACAGATGGTCATGGTTATGCTTTCCCCTATTCACTTGCTGATCTCAATTTGAACAGTAA
AAATGGTTACATCGTAAAAGACTTGTTTAACCTTAAGCGAAAAACATTCAATCTGTTGCA
AAATGAAACGCATGAAGAAAGAGTTAATCCTACGGGTGCCAATTTCTATAAATTTACTCC
TATCAAGTAA
>g5260.t2 Gene=g5260 Length=162
NDPDTLLLGNFGLSYEQSKAQLAIWAVIAAPFLLSNDLRTVTPEIKELLLNREIIAVDQD
PLGIQGKQLKKGNGIEVWVRPITPIVGNEYSYAVAFVSRRTDGHGYAFPYSLADLNLNSK
NGYIVKDLFNLKRKTFNLLQNETHEERVNPTGANFYKFTPIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5260.t2 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 1 | 62 | 0 |
| 8 | g5260.t2 | Gene3D | G3DSA:2.60.40.1180 | - | 63 | 162 | 0 |
| 3 | g5260.t2 | PANTHER | PTHR11452 | ALPHA-GALACTOSIDASE/ALPHA-N-ACETYLGALACTOSAMINIDASE | 1 | 161 | 0 |
| 4 | g5260.t2 | PANTHER | PTHR11452:SF66 | ALPHA-GALACTOSIDASE | 1 | 161 | 0 |
| 2 | g5260.t2 | Pfam | PF16499 | Alpha galactosidase A | 1 | 60 | 0 |
| 1 | g5260.t2 | Pfam | PF17450 | Alpha galactosidase A C-terminal beta sandwich domain | 63 | 152 | 0 |
| 6 | g5260.t2 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 1 | 61 | 0 |
| 5 | g5260.t2 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 62 | 161 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5260/g5260.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5260.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0003824 | catalytic 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. There were no conditions that were differentially expressed