This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison
Closest relative of CDH23 in c. elegans
There is no database record of a homologue gene for CDH23 in c. elegans. Instead we have provided the c. elegans' gene whose product best aligns with human cdh23 protein:
1#status:Confirmed#UniProt:Q965J5#protein_id:AAC17530.3
Length = 441
[Gene Summary][Protein Summary]
Score = 612 bits (1577), Expect = e-175, Method: Composition-based stats.
Identities = 331/441 (75%), Positives = 331/441 (75%)
Query: 1 MNHIDLLKVXXXXXXXXXXXXXXXXXXHTIEGILDIRKKEMNVSDLMCTRXXXXXXXXXV 60
MNHIDLLKV HTIEGILDIRKKEMNVSDLMCTR V
Sbjct: 1 MNHIDLLKVKKEPPSSSEEAEEEESPKHTIEGILDIRKKEMNVSDLMCTRSSTPPTSSSV 60
Query: 61 DSIITLWQFLLELLQQDQNGDIIEWTRGTDGEFRLIDAEAVARKWGQRKAKPHMNYDKLS 120
DSIITLWQFLLELLQQDQNGDIIEWTRGTDGEFRLIDAEAVARKWGQRKAKPHMNYDKLS
Sbjct: 61 DSIITLWQFLLELLQQDQNGDIIEWTRGTDGEFRLIDAEAVARKWGQRKAKPHMNYDKLS 120
Query: 121 RALRYYYEKNIIKKVIGKKFVYRFVTTDAHAPPTADFSSNMNMKMCYVKDEKDIRHEIPS 180
RALRYYYEKNIIKKVIGKKFVYRFVTTDAHAPPTADFSSNMNMKMCYVKDEKDIRHEIPS
Sbjct: 121 RALRYYYEKNIIKKVIGKKFVYRFVTTDAHAPPTADFSSNMNMKMCYVKDEKDIRHEIPS 180
Query: 181 FMTSLQAXXXXXXXXQNPRGNTDFSALSLLGXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240
FMTSLQA QNPRGNTDFSALSLLG
Sbjct: 181 FMTSLQAPPPPPPPPQNPRGNTDFSALSLLGTDSPTTHSVSTPSPTDSVCSPSSSVASSA 240
Query: 241 XXXXXXXXDESRQCRKRXXXXXXXXXXXXXXXXXXXXXKKGMKPNPLNLTATSNFSLQPS 300
DESRQCRKR KKGMKPNPLNLTATSNFSLQPS
Sbjct: 241 TPSTSSPVDESRQCRKRSLSPSTTSSTTAPPPPPQPPTKKGMKPNPLNLTATSNFSLQPS 300
Query: 301 ISSPLLMLQQHHQNSPLFQAQISQLYTYAALASAGLYGPQISPHLASQSPFRSPLVTPKN 360
ISSPLLMLQQHHQNSPLFQAQISQLYTYAALASAGLYGPQISPHLASQSPFRSPLVTPKN
Sbjct: 301 ISSPLLMLQQHHQNSPLFQAQISQLYTYAALASAGLYGPQISPHLASQSPFRSPLVTPKN 360
Query: 361 LGLGELGSSGRTPGLGESQVFQFPPVSAFQATNPLLNTFSNLISPMAPFMMXXXXXXXXX 420
LGLGELGSSGRTPGLGESQVFQFPPVSAFQATNPLLNTFSNLISPMAPFMM
Sbjct: 361 LGLGELGSSGRTPGLGESQVFQFPPVSAFQATNPLLNTFSNLISPMAPFMMPPSQSSTSF 420
Query: 421 XXXXXXXXLKTPTVPIKMPTL 441
LKTPTVPIKMPTL
Sbjct: 421 KFPSSTDSLKTPTVPIKMPTL 441
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- Most closely related gene in c. elegans: unc-26, which has a 441 AA gene product.
- 75% homology by alignment, effective e=0.
- Ortholog of this gene in C. elegans: C34B7.2sac-1W09C5.7
- Report of gene alignment:
1#status:Confirmed#UniProt:Q965J5#protein_id:AAC17530.3
Length = 441
[Gene Summary][Protein Summary]
Score = 612 bits (1577), Expect = e-175, Method: Composition-based stats.
Identities = 331/441 (75%), Positives = 331/441 (75%)
Query: 1 MNHIDLLKVXXXXXXXXXXXXXXXXXXHTIEGILDIRKKEMNVSDLMCTRXXXXXXXXXV 60
MNHIDLLKV HTIEGILDIRKKEMNVSDLMCTR V
Sbjct: 1 MNHIDLLKVKKEPPSSSEEAEEEESPKHTIEGILDIRKKEMNVSDLMCTRSSTPPTSSSV 60
Query: 61 DSIITLWQFLLELLQQDQNGDIIEWTRGTDGEFRLIDAEAVARKWGQRKAKPHMNYDKLS 120
DSIITLWQFLLELLQQDQNGDIIEWTRGTDGEFRLIDAEAVARKWGQRKAKPHMNYDKLS
Sbjct: 61 DSIITLWQFLLELLQQDQNGDIIEWTRGTDGEFRLIDAEAVARKWGQRKAKPHMNYDKLS 120
Query: 121 RALRYYYEKNIIKKVIGKKFVYRFVTTDAHAPPTADFSSNMNMKMCYVKDEKDIRHEIPS 180
RALRYYYEKNIIKKVIGKKFVYRFVTTDAHAPPTADFSSNMNMKMCYVKDEKDIRHEIPS
Sbjct: 121 RALRYYYEKNIIKKVIGKKFVYRFVTTDAHAPPTADFSSNMNMKMCYVKDEKDIRHEIPS 180
Query: 181 FMTSLQAXXXXXXXXQNPRGNTDFSALSLLGXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 240
FMTSLQA QNPRGNTDFSALSLLG
Sbjct: 181 FMTSLQAPPPPPPPPQNPRGNTDFSALSLLGTDSPTTHSVSTPSPTDSVCSPSSSVASSA 240
Query: 241 XXXXXXXXDESRQCRKRXXXXXXXXXXXXXXXXXXXXXKKGMKPNPLNLTATSNFSLQPS 300
DESRQCRKR KKGMKPNPLNLTATSNFSLQPS
Sbjct: 241 TPSTSSPVDESRQCRKRSLSPSTTSSTTAPPPPPQPPTKKGMKPNPLNLTATSNFSLQPS 300
Query: 301 ISSPLLMLQQHHQNSPLFQAQISQLYTYAALASAGLYGPQISPHLASQSPFRSPLVTPKN 360
ISSPLLMLQQHHQNSPLFQAQISQLYTYAALASAGLYGPQISPHLASQSPFRSPLVTPKN
Sbjct: 301 ISSPLLMLQQHHQNSPLFQAQISQLYTYAALASAGLYGPQISPHLASQSPFRSPLVTPKN 360
Query: 361 LGLGELGSSGRTPGLGESQVFQFPPVSAFQATNPLLNTFSNLISPMAPFMMXXXXXXXXX 420
LGLGELGSSGRTPGLGESQVFQFPPVSAFQATNPLLNTFSNLISPMAPFMM
Sbjct: 361 LGLGELGSSGRTPGLGESQVFQFPPVSAFQATNPLLNTFSNLISPMAPFMMPPSQSSTSF 420
Query: 421 XXXXXXXXLKTPTVPIKMPTL 441
LKTPTVPIKMPTL
Sbjct: 421 KFPSSTDSLKTPTVPIKMPTL 441
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*Produced by Wormbank BLAST
Expression of protein in c. Elegans
UNC-26 is expressed in the reproductive system, uterine muscle, vulvul muscle, anal depressor muscle, and body wall muscle in grown c. Elegans.
Gene ontologies of unc-26 protein in c. Elegans
None of the gene ontologies for the chosen c. Elegans' protein matched GOs for human CDH23 ptrotein. Therefore, as a model organism c. Elegans would be a bad choice for researching Usher Syndrome
Corresponding Protein Sequence in c. Elegans:
| unc-26_protein_sequ..docx |
*expression and GOs found on UNC-26 gene summary
References:
1. Wormbase BLAST:http://www.wormbase.org/db/searches/blat
2. Gene Summary for UNC-26: http://www.wormbase.org/db/gene/gene?name=WBGene00006763;class=Gene
1. Wormbase BLAST:http://www.wormbase.org/db/searches/blat
2. Gene Summary for UNC-26: http://www.wormbase.org/db/gene/gene?name=WBGene00006763;class=Gene
Ben Hofeld, [email protected], last updated: 5.15.2010, Link to course page:www.gen677.weebly.com
