General information for g10852.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hexosaminidase D.
Parent gene
- The parent gene g10852 is located on chr_1: 12280550..12287581 (+ 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 | g10852 | g10852.t1 | TSS | g10852.t1 | 12279920 | 12279920 |
| chr_1 | g10852 | g10852.t1 | isoform | g10852.t1 | 12280550 | 12287581 |
| chr_1 | g10852 | g10852.t1 | exon | g10852.t1.exon1 | 12280550 | 12280576 |
| chr_1 | g10852 | g10852.t1 | cds | g10852.t1.CDS1 | 12280550 | 12280576 |
| chr_1 | g10852 | g10852.t1 | exon | g10852.t1.exon2 | 12284964 | 12285107 |
| chr_1 | g10852 | g10852.t1 | cds | g10852.t1.CDS2 | 12284964 | 12285107 |
| chr_1 | g10852 | g10852.t1 | exon | g10852.t1.exon3 | 12285530 | 12285665 |
| chr_1 | g10852 | g10852.t1 | cds | g10852.t1.CDS3 | 12285530 | 12285665 |
| chr_1 | g10852 | g10852.t1 | exon | g10852.t1.exon4 | 12285730 | 12285923 |
| chr_1 | g10852 | g10852.t1 | cds | g10852.t1.CDS4 | 12285730 | 12285923 |
| chr_1 | g10852 | g10852.t1 | exon | g10852.t1.exon5 | 12285983 | 12287581 |
| chr_1 | g10852 | g10852.t1 | cds | g10852.t1.CDS5 | 12285983 | 12287581 |
| chr_1 | g10852 | g10852.t1 | TTS | g10852.t1 | 12287600 | 12287600 |
Sequences
>g10852.t1 Gene=g10852 Length=2100
ATGATTAAAACTTTGATTCTAAAAAAGATGCATTCGCGTTTTTTGGTGCTTGTTTGCCGG
AAAAAGTTGTTATTGGTTGCAGTAGCCTTCCTTGTGTCGATTATATGGGGATTTATTTAT
TCATCGACTACTAGCGGGCATGATGATACAAACAAAGGTGTTTCAGTGAAGGATAGAAAA
CTAGAAAATAAGTATGAGTTATTGCAAAAACTTGCTGTAAACCAAAAAGATGTAAATGAA
CCGCTTCGATATTTATTCAAACCAACTGCCATAAATCTTCAAACTCTTCATGATCTAAAC
CGAAGAGAAAAATATTTCAAAGATTGGAATAAAATCCTCCTTGACAAGGAAGAAAAAGAA
AGAATTGAAAATTTTGCAATTATTTCACGCGATGAGATATCACGTAGAAAGATAGCGGAT
GAAATGAAAGTGGCAGCCGACAGACAAGCAAAGTATGAAGGTCAATTGAAGAAAATGGGA
ATACCTGTAATTGTTGGATTGGGACCGACAAATCGTCACAAGCCACCTGAACAAGTTCTC
GTACACTTCGACCTCAAGGGAGCTCCAATGAAAGTCAGTTACATTTTGAAAATGCTGTCA
ATGATTAAAACACTTGGAGCGACAGGAATAATTTTAGAGTATGAAGATACATTTCCCTAT
AGTGATACATTATCAGGCATTACAGCAAAAAATGCTTATAGCAAAAAAAATATCATTGAA
ATTTTACAAACGGCATATGCATTAAATCTTAAAGTCATTCCATTAGTTCAAACATTTGGT
CATTTGGAATTTGTGCTAAAATTGAAGGAATTTCAACATTTAAGAGAAGTTCAAGAAGCA
CCACAATCGATTTGTCCTAGTTTGAATTCGTCCTTCACCTTCATTGAAGAACTTCTGACA
CAAGTTATAAATCTTCATACACTAAATCAACAACAGCAAAGAATTTTAATGAATCGTAAT
GATCGTGAGAATAATGATGATAACGATAGAGATATTCCAGAAATGACACATATACATATC
GGCTGTGATGAAGTTTATCAATTGGGTACATGCAATAGATGTCGTGAAAGAGTTCATGAT
ACATTATTTTTAGACCATGTTTATAATGTTGCAGCCTTTGTCAAAAAGAAATGGCCAAAA
TTAAATGTCATTATCTGGGACGATCAACTTCGTGGAATGACAACTGAGACTTTAAGAGCA
TCAGGCATAGGAAGAATGGTTGAACCAATGATTTGGGCATATACTGAGGATATTTATAAA
TTCATATCTTCATTGATATGGGACAAATATTCTCAAGTTTTTAAGACAGCATGGGTTGCA
GGAGCGTTTAAGGGAGCATTTGGTGAGACACTTTTGATTCCACAAGGAAGAAGACATTTG
GAAAATACACTTCGATGGTTGGCAATTATTCAAGGTGAAGGAACAAGGTTTCAAGAGGGA
ATATGTGGAATAGTTTTAACAGGCTGGTCACGTTATGACCATTTTGCCGTACTCTGTGAA
TTATTCCCTGCATCAATACCATCCCTCGCTCTGTGTCTTCATACAGCTGCTTTAGGATAT
TTTGAAATTGATTCAAAATCAAATTCAATTATTCCGAGTCTTACATGTCCCGATGCAAAA
GGTGATCGATATTTATGGCTTGACCTTCAAAAAGATCCAAATCTAAATGCATTTTCGCGT
TGCATATTTCCTGGTAGTTCCGTTTTTCGATATATAAATCGACTTTCTTCAATCACACAA
GAAACACGCGAATTTATTGATTCAATTAAATATTCTCGTGGTTGGTTATCAGACTATAAT
ATTCGGCACAATTATACATCATCATCTCGTGTTTTAGAACTTCTTGAAGATCAACCGAGA
TTATTAGCATCTTTATTAAATTTAGCTCGTAGCATAGCTGAAGCAATGGAAGAGATGTAT
GATCATTTTACAATTGGTGAATATATTGAGCAACGCGTGTATCCATTAGTGAATGAATTA
AAAAGTTTGGAAAAGGTTGGTGAGAGTTTGAGAATGAGAAAAGTTTTTCCCGTTCGACCA
CTTCCATATCTAGAAAAGTTCATTAAAGAACTTGGCATCACGCAGCGAACACCCAATTAA
>g10852.t1 Gene=g10852 Length=699
MIKTLILKKMHSRFLVLVCRKKLLLVAVAFLVSIIWGFIYSSTTSGHDDTNKGVSVKDRK
LENKYELLQKLAVNQKDVNEPLRYLFKPTAINLQTLHDLNRREKYFKDWNKILLDKEEKE
RIENFAIISRDEISRRKIADEMKVAADRQAKYEGQLKKMGIPVIVGLGPTNRHKPPEQVL
VHFDLKGAPMKVSYILKMLSMIKTLGATGIILEYEDTFPYSDTLSGITAKNAYSKKNIIE
ILQTAYALNLKVIPLVQTFGHLEFVLKLKEFQHLREVQEAPQSICPSLNSSFTFIEELLT
QVINLHTLNQQQQRILMNRNDRENNDDNDRDIPEMTHIHIGCDEVYQLGTCNRCRERVHD
TLFLDHVYNVAAFVKKKWPKLNVIIWDDQLRGMTTETLRASGIGRMVEPMIWAYTEDIYK
FISSLIWDKYSQVFKTAWVAGAFKGAFGETLLIPQGRRHLENTLRWLAIIQGEGTRFQEG
ICGIVLTGWSRYDHFAVLCELFPASIPSLALCLHTAALGYFEIDSKSNSIIPSLTCPDAK
GDRYLWLDLQKDPNLNAFSRCIFPGSSVFRYINRLSSITQETREFIDSIKYSRGWLSDYN
IRHNYTSSSRVLELLEDQPRLLASLLNLARSIAEAMEEMYDHFTIGEYIEQRVYPLVNEL
KSLEKVGESLRMRKVFPVRPLPYLEKFIKELGITQRTPN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g10852.t1 | CDD | cd06565 | GH20_GcnA-like | 178 | 513 | 2.77032E-113 |
| 6 | g10852.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 184 | 514 | 1.1E-65 |
| 2 | g10852.t1 | PANTHER | PTHR21040:SF8 | BCDNA.GH04120 | 126 | 687 | 1.6E-186 |
| 3 | g10852.t1 | PANTHER | PTHR21040 | UNCHARACTERIZED | 126 | 687 | 1.6E-186 |
| 1 | g10852.t1 | Pfam | PF00728 | Glycosyl hydrolase family 20, catalytic domain | 228 | 394 | 1.5E-5 |
| 8 | g10852.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 46 | - |
| 9 | g10852.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 22 | - |
| 10 | g10852.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 23 | 34 | - |
| 11 | g10852.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 35 | 46 | - |
| 7 | g10852.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 47 | 699 | - |
| 5 | g10852.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 181 | 515 | 1.18E-42 |
| 4 | g10852.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 23 | 40 | - |
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:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0015929 | hexosaminidase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14459 (hexosaminidase)
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.
