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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag

Basic information

species Physcomitrella patens
transcript PP1S114_48V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 5'ss of exon 4
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgt-gttccag---
|||||||||||| || ||||| |||||| |||||||||| || ||||||||||||||||| ||    || ||  |  ||||| | || ||||| || |||||  |    ||  |||      ||||    |     |  |  ||| |||  ||    ||| |  |  | |     ||||||| | | |   |   
CGGTCAACAAGGCTCATACCCAATTAAGCTGTTCTACACTTCAAACATGCCCATCATTCTGCATTCTGCACTGATTACCAACCTCTATTTCATATCCCAGgtctgaacttcaattcc-----actgcttta-----gcaagataaatctttaatgtttgtgt-ttagcattaacatgtttgtattgctttggcag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os09g17840.1 (Oryza sativa), 5'ss of exon 3
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctctctgttcttgttgact--gtcgcattcgtgt---caagtaattctgaaagacgtgtctactca----cttgcttttgtttgtgt-gttccag
 || || ||||| || || || ||||||||||||||||| || ||||||||||||||||| ||    || ||  |  ||||| | |||||||| |||||||| ||        || | || |  |  ||   |||    |     || || | | ||     |  ||   ||     |  | | | ||| | | ||| |||
GGGGCAGCAAGGCTCATATCCAATTAAGTTGTTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctgtaattgtagtggctttagtaatatttacatgactgagcaagttttaacatgataactgagcaagttttaacatatatttattttgttgcag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 5'ss of exon 3
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag
 || || ||||| || || || ||||||||||||||||| || ||||||||||||||||| ||    || ||  |  ||||| | |||||||| |||||||| ||    |  | | |||| |  || |||| |  | |  |  | | ||||   | || | ||   || || |||| |||   |||| |||
GGGGCAGCAAGGCTCATATCCAATTAAGTTGTTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcg----tgcggtattgtag--tgccgcagtaatattta-cattactgatcaa-gttttta---acatgtttttattt---tgttgcag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GRMZM2G307252_T02 (Zea mays), 5'ss of exon 4
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcact-tgcttttgtttgtgtgttccag
 ||||||||||| || ||||| || ||||||||||| || ||||||||||| |||||||| ||    || ||  |  ||||| | || ||||| || |||||  |    ||  |||  ||     ||  ||||    |  |    |||   ||   |  |  ||| |   || || | |    |        
TGGTCAACAAGGCTCATACCCAATCAAGTTGTTCTATACTTCCAACATGCCTATCATTCTGCACTCTGCACTAATTACCAACCTCTATTTCATATCCCAGgtatgtgcttcaattccagt-----gtttcattacaattgatcttttcatgaatttgcatggactaaaaatgtttctatggcag--------

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA13G34370.1 (Glycine max), 5'ss of exon 4
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgt---tcgcctctctgttcttgttgact-gtcgcattcgtgtcaagtaattctgaaagacgtgtctactc-acttgcttttgtttgtgtgttccag
 || || || || || || || || || ||||| || ||||||||||||||||||||||| |||   |||||||| |||||  | |||||||| || |||||   |   || | || |    | ||||    |  || |  |  | |  || | | || |   | || || ||||| |                  
TGGACAGCAGGGTTCATATCCAATCAAATTGTTTTATACCTCCAACATGCCCATCATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATCTCCCAGgtaattaagctgtatgataggttggacttaatgtttttggatttattg-ttttaacagtctaatttattctacttgttcag---------------

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA12G17950.1 (Glycine max), 5'ss of exon 4
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgtt-cgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag
 || || || || || || || || ||||| || || ||||||||||||||||| ||||| |||   |||||||| |||||  | ||||||||||| |||||   |    |   || | ||  | |||| | || | || || |  | ||        ||| |  |||   | ||||  | |  |  | |||
TGGACAGCAGGGGTCGTATCCAATCAAGTTATTTTATACCTCCAACATGCCCATTATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATTTCTCAGgtagtggagtttaattatggtaaattgtcac-ttggagtaaaattttgctac------tgttttatcaa--gattttactggatttgtacag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: GLYMA06G32680.1 (Glycine max), 5'ss of exon 4
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgtt-cgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag
 || || || || ||||| || || ||||| || || ||||||||||||||||| ||||| |||   |||||||| |||||  | ||||||||||| |||||   |    |   |  | ||  | |||| | || | || ||   ||| ||  |    ||| |   || |   |||  |   | ||| |   
TGGACAGCAGGGGTCTTATCCAATCAAGTTATTTTATACCTCCAACATGCCCATTATTCTTCAGTCTGCCCTTGTTTCCAATCTCTACTTCATTTCTCAGgtagtggagtttaatgatggtaaattgtcac-ttggagtaaa---attttgttat---tgttttaacaat-attttaatggatttgtacag-

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT1G78720.1 (Arabidopsis thaliana), 5'ss of exon 3
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag---
 || |||| ||| ||||| ||||| || ||||||||||||||||||||||| |||||  | |||   || ||||| |||||  | |||||||| || |||||    |  |||   | |  |     |   ||  ||    | || |     |||   | | |||| |    | || ||   | |||| |     
TGGACAACGAGGCTCTTATCCTATCAAATTGTTCTACACCTCCAACATGCCTATCATCTTGCAGTCAGCTCTTGTTTCCAATATCTACTTCATCTCTCAGgt--atcaatctacacatagt---ctttaaatctgtacttaatatt----gaagctctttatacttaaaaacgtt-gtgaatctgtttctatag

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv18s0076g00240.t01 (Vitis vinifera), 5'ss of exon 1
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcct-ctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag
 || |||||||| || || ||||||||||||||||||||||||||||||||||||||||| ||    || ||||| |||||| | ||||| || ||  |||| |     || |   |||||  ||    | |||   ||||  |  |||||   |   |    ||    ||  || |  | |          
TGGACAACAAGGTTCATATCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTACAATTTGCTCTTGTTTCCAACATTTACTTTATATCCTAGgtacttgagctttaagcttgtataca--tgaattgcagtcattttcttctggt-gttatactaacaattttatttcttatag----------

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv19s0014g01020.t01 (Vitis vinifera), 5'ss of exon 4
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcct-ctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag
 || || || || || || ||||||||| ||||||||||||||||||||||||||||| | |||   || ||||| |||||| | ||||| || || ||||| |     || |   |||||  ||    |  ||   ||||  |  |||||   |   |    ||    ||  || |    |          
TGGACAGCAGGGTTCATATCCTATTAAGCTGTTCTACACCTCCAACATGCCCATCATTTTACAGTCTGCTCTTGTTTCCAACCTTTACTTTATATCCCAGgtacttgagctttaagcttgtataca--tgagttgcggtcattttcttctggt-gttatactaacaattttatttcttacag----------

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: Vv00s0551g00030.t01 (Vitis vinifera), 5'ss of exon 1
CGGTCAACAAGGATCTTACCCTATTAAGTTGTTCTACACCTCCAACATGCCCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgt-tcgcctctctgttcttgttgactgtcgcattcgtgtcaagtaattctgaaagacgtgtctactcacttgcttttgtttgtgtgttccag
 || || || || || || ||||| ||| ||||||||||||||||||||||||||||||| |||   || |||||  ||||| | ||||| || || |||||   |   || |   |||||  ||   |   || | ||||  |  |||||   |   |    ||    ||  || |    |          
TGGACAGCAGGGTTCATATCCTATCAAGCTGTTCTACACCTCCAACATGCCCATCATTCTACAGTCTGCTCTTGTTACCAACCTATACTTTATATCCCAGgtactggagctttaagcttgtataca--caggttggggtcattttcttctggt-gttatactaacaattttatttcttacag----------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|208368248|gb|DC951514.1|DC951514
EST:     CAACTTGTACTTCATTTCACAG                         CTATTGTTCAAGAGATACAGCAACAATTTCGTTGTGAATCTTCTTGGAAAG
genomic: CAACTTGTACTTCATTTCACAGgttcgcctct ... tgtgttccagCTATTGTTCAAGAGATACAGCAACAATTTCGTTGTGAATCTTCTTGGAAAG
EST: gi|208388528|gb|DC957082.1|DC957082
EST:     CCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAG                         CTATTGTTCAAGAGATACAGCAACAATTTCGTTGTGAATCTTCTTGGAAAG
genomic: CCATCATTCTCCAGAGCGCCCTTGTCTCCAACTTGTACTTCATTTCACAGgttcgcctct ... tgtgttccagCTATTGTTCAAGAGATACAGCAACAATTTCGTTGTGAATCTTCTTGGAAAG