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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCATTCGGGTCAAGCTCGCGTGGAGGATTCGCAATGGCAAGCGTTGCAGCGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacggattctatctctctctctctcagtgggtcgcttgttgctttgtatctgtttcctgtcctatcctccgattttctacggtatggcggattg...

Basic information

species Physcomitrella patens
transcript PP1S50_182V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S50_182V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os02g57854.1 (Oryza sativa), 5'ss of exon 2
AGCATTCGGGTCAAGCTCGCGTGGAGGATTCGCAATGGCAAGCGTTGCAGCGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacggattctatctctctctctctcagtgggtcgcttgttgctttgtatctgtttcct-gtcctatcctccgattttctacggtatggcggattg----
                |    | |   | |  | |||||  | |  ||   |||  |  || |     ||||  | ||||||||||||||||||||||||||| |||||     | | |  |  ||   |   || | | |   |        | ||  |   | | || |  |      |  || | | || || || ||    
----------------TTAGTTAGTTAAGTTTCCATGGCGGG-GAGGCCCAGCATCC--CGACCAACAGCTCCGCTCTCATCGCCATCATCGCCGACGAGgtacgccac----cccaacattagcttcatgtttgcgcc-ccaatcataccacaactcctgaatagccccaatcataccatacctcctgaattgccgaatgccca

upper sequence: PP1S50_182V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: LOC_Os04g05080.1 (Oryza sativa), 5'ss of exon 2
AGCATTCGGGTCAAGCTCGCGTGGAGGATTCGCAATGGCAAGCGTTGCAGCGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacggattctatctctctctctctcagtgggtcgcttgttgctttgtatctgttt--cctgtcctatcctccgattttctacggtatggcggattg----
                         |   |||| |||||  | |  ||   |||  |  || |     ||||  ||||||||||||||||||||||||||||| |  || |   | | | | | |   |||       ||| |    |||||  | || ||  | || |  ||  | |    | |||| |  ||     |||    
-------------------------GAGGTCGCCATGGCGGG-GAGGCCCAGCATCC--CGACCAACAGCTCTGCGCTCATCGCCATCATCGCCGACGAGgta-gttacag---ccaccccccacctcctcccctttccgccttgctctttgcctttgcttggcttggctgattgtgccgcct-ctaccgc-tgctcttttgctac
















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|162264736|gb|FC440303.1|FC440303
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|15261878|gb|BI437188.1|BI437188
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|67571243|gb|BJ944067.1|BJ944067
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|162237446|gb|FC412749.1|FC412749
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|67576299|gb|BJ949123.1|BJ949123
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|67699809|gb|BJ960042.1|BJ960042
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|162237445|gb|FC412748.1|FC412748
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCTGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
EST: gi|67694560|gb|BJ954793.1|BJ954793
EST:     CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAG                         GATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC
genomic: CGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 19 (upstream exon), 28 (downstream exon)
Score: 2

AGCATTCGGGTCAAGCTCGCGTGGAGGATTCGCAATGGCAAGCGTTGCAGCGCAAGCGTCGTCACGGGGCTCATCGCTCATCGCCATCATCGCCGACGAGgtatgccacg ... cttttggcagGATACAGTAACAGGATTTTTGCTAGCAGGTGTGGGCAATGTAGACCTACGCCGAAAGACCAACTACCTAGTTGTGGACAACA




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