General information for g5260.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | isoform | g5260.t1 | 8286298 | 8288636 |
| chr_2 | g5260 | g5260.t1 | exon | g5260.t1.exon1 | 8286298 | 8286787 |
| chr_2 | g5260 | g5260.t1 | cds | g5260.t1.CDS1 | 8286298 | 8286787 |
| chr_2 | g5260 | g5260.t1 | exon | g5260.t1.exon2 | 8286906 | 8287106 |
| chr_2 | g5260 | g5260.t1 | cds | g5260.t1.CDS2 | 8286906 | 8287106 |
| chr_2 | g5260 | g5260.t1 | exon | g5260.t1.exon3 | 8287164 | 8287387 |
| chr_2 | g5260 | g5260.t1 | cds | g5260.t1.CDS3 | 8287164 | 8287387 |
| chr_2 | g5260 | g5260.t1 | exon | g5260.t1.exon4 | 8287454 | 8287583 |
| chr_2 | g5260 | g5260.t1 | cds | g5260.t1.CDS4 | 8287454 | 8287583 |
| chr_2 | g5260 | g5260.t1 | exon | g5260.t1.exon5 | 8287648 | 8287766 |
| chr_2 | g5260 | g5260.t1 | cds | g5260.t1.CDS5 | 8287648 | 8287766 |
| chr_2 | g5260 | g5260.t1 | exon | g5260.t1.exon6 | 8288559 | 8288636 |
| chr_2 | g5260 | g5260.t1 | cds | g5260.t1.CDS6 | 8288559 | 8288636 |
| chr_2 | g5260 | g5260.t1 | TSS | g5260.t1 | 8289004 | 8289004 |
| chr_2 | g5260 | g5260.t1 | TTS | g5260.t1 | NA | NA |
Sequences
>g5260.t1 Gene=g5260 Length=1242
ATGAAGAGCATCATTATTATTTTCTGTATCTACATTTCAATCGCACGAGCCCTCGATAAT
GGCTTGGCAAAAACACCGCCAATGGGATGGATGAGTTGGGAACGATTTCGATGTATTATC
GATTGTGATAAATATCCTGATGAGTGCATTAGTGAGCGACTAATTATAGAGATGGCTGAT
ATAATGGTAAAGGATGGTTATCTCGCTGCTGGCTATGAATATGTAAATATCGATGATTGT
TGGAGTGAATTGGAACGCGATAAAGATGGTAAAATTATTGCTGACAAGAATCGATTCCCT
CGTGGCATTAAATTCCTGTCAGATTATGTTCATTCAAAAGGATTGAAATTTGGCACGTAT
CTTGATTATGGCACAAAAACATGCGCCGGTTATCCAGGATCACTCGACTTTTTAGAGACA
GATGCACAATCTTTAGCCGAATGGGAAGTTGATTTTATAAAGATGGATGGCTGTAATGTT
GACACTGAGAAGATGGTTGATGGATATATTGAATTTGGAAGGTTGATGAATGCGACTGGC
AGACCGATAATGTATTCATGCTCATGGCCAGCATATTTTGAATATTATAGAAAGCCTACA
ATGTATCCTGATTATGAAATTTTAAAGAAAACTTGTAACCTTTGGAGAAATTGGAAAGAT
ATTGAAGATAGTTATGAATCAATGCTTTTTACATCTGATTATTTTGCTGAACATGCTGAA
AGAGTTGCACCGCATGCTGGACCAGGTCATTGGAATGATCCAGACACTCTTCTACTTGGA
AATTTTGGCCTAAGTTACGAACAAAGTAAAGCACAATTGGCAATTTGGGCAGTTATTGCT
GCTCCATTTCTCTTATCAAATGATCTTAGGACTGTCACACCGGAAATTAAAGAACTTTTA
CTTAATCGAGAAATTATCGCAGTTGACCAAGATCCACTTGGTATTCAAGGTAAACAACTA
AAGAAGGGTAATGGAATTGAAGTATGGGTGAGACCAATAACACCAATTGTCGGAAATGAA
TACTCGTATGCTGTTGCATTTGTTTCAAGACGTACAGATGGTCATGGTTATGCTTTCCCC
TATTCACTTGCTGATCTCAATTTGAACAGTAAAAATGGTTACATCGTAAAAGACTTGTTT
AACCTTAAGCGAAAAACATTCAATCTGTTGCAAAATGAAACGCATGAAGAAAGAGTTAAT
CCTACGGGTGCCAATTTCTATAAATTTACTCCTATCAAGTAA
>g5260.t1 Gene=g5260 Length=413
MKSIIIIFCIYISIARALDNGLAKTPPMGWMSWERFRCIIDCDKYPDECISERLIIEMAD
IMVKDGYLAAGYEYVNIDDCWSELERDKDGKIIADKNRFPRGIKFLSDYVHSKGLKFGTY
LDYGTKTCAGYPGSLDFLETDAQSLAEWEVDFIKMDGCNVDTEKMVDGYIEFGRLMNATG
RPIMYSCSWPAYFEYYRKPTMYPDYEILKKTCNLWRNWKDIEDSYESMLFTSDYFAEHAE
RVAPHAGPGHWNDPDTLLLGNFGLSYEQSKAQLAIWAVIAAPFLLSNDLRTVTPEIKELL
LNREIIAVDQDPLGIQGKQLKKGNGIEVWVRPITPIVGNEYSYAVAFVSRRTDGHGYAFP
YSLADLNLNSKNGYIVKDLFNLKRKTFNLLQNETHEERVNPTGANFYKFTPIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g5260.t1 | CDD | cd14792 | GH27 | 26 | 311 | 3.68712E-133 |
| 15 | g5260.t1 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 18 | 313 | 2.6E-115 |
| 16 | g5260.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 314 | 413 | 3.4E-23 |
| 3 | g5260.t1 | PANTHER | PTHR11452 | ALPHA-GALACTOSIDASE/ALPHA-N-ACETYLGALACTOSAMINIDASE | 6 | 412 | 1.0E-181 |
| 4 | g5260.t1 | PANTHER | PTHR11452:SF66 | ALPHA-GALACTOSIDASE | 6 | 412 | 1.0E-181 |
| 11 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 20 | 39 | 5.9E-51 |
| 9 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 66 | 81 | 5.9E-51 |
| 8 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 107 | 128 | 5.9E-51 |
| 6 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 141 | 158 | 5.9E-51 |
| 5 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 168 | 186 | 5.9E-51 |
| 7 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 246 | 265 | 5.9E-51 |
| 10 | g5260.t1 | PRINTS | PR00740 | Glycosyl hydrolase family 27 signature | 267 | 288 | 5.9E-51 |
| 2 | g5260.t1 | Pfam | PF16499 | Alpha galactosidase A | 25 | 311 | 7.4E-132 |
| 1 | g5260.t1 | Pfam | PF17450 | Alpha galactosidase A C-terminal beta sandwich domain | 314 | 403 | 4.1E-15 |
| 18 | g5260.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 19 | g5260.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 20 | g5260.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 21 | g5260.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 17 | g5260.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 413 | - |
| 23 | g5260.t1 | ProSitePatterns | PS00512 | Alpha-galactosidase signature. | 71 | 87 | - |
| 13 | g5260.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 18 | 312 | 3.19E-87 |
| 12 | g5260.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 313 | 412 | 9.35E-15 |
| 14 | g5260.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5260/g5260.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5260.t1.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 transcript has been annotated with K01189 (alpha-galactosidase)
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.
