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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgtttcattgcaacctggttcactgtgtgttgcgttgtttcggtagagttgttgtgcggtcgagtttcgggttgccccaaaaaaagagagctgagagtcgtgtgttgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA

Basic information

species Physcomitrella patens
transcript PP1S13_236V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g52490.1 (Oryza sativa), 3'ss of exon 2
gtgtgtgtttcattgcaacctggttcactgtgtgttgcgttgtttcggtagagttgttgtgcggtcgagtttcgggttgccccaaaaaaagagagctgagagtcgtgtgttgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA
                               |||   | | | |   ||| |  |    || ||| | | |   | ||  |         |          |  | |  ||       ||||||||||||||||| |||||||| |||||||||||||| |  ||  |  |   |||||| ||||||  |||| | || || ||||| || ||||||||||
-------------------------------gtgagacctcggt---gtaaatcttacatgtggtggtggtgatgatttgcggggggtttggatctcagcggctggggttttgctgtgcagGCTGAGCTGAAGGAGAAGCTGGCCAAGCTGTACGAGGTGAAGGACGCGAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGTGGAGGCAAGTCCA

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g36160.1 (Oryza sativa), 3'ss of exon 1
gtgtgtgtttcattgcaacctggttcactgtgtgttgcgttgtttcggtagagttgttgtgcggtcgagtttcgggttgccccaaaaaaagagagctgagagtcgtgtgttgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA
                             ||| ||| ||||  |  |||   |     ||| ||  |||    |||  |     |   | |          ||  ||||    |    ||||| || |||||||| |||||||| |||||||||||||| |  ||  || |   |||||| ||||||  |||| | || || |||||||| ||||||||||
-----------------------------gtgcgtttcgtt--tagggtttcgcccgcgtgagggtgaggggaggg--ggagagagcgaggctgatccgctgtattgtgcgcgttgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGCGGCAAGTCCA

upper sequence: PP1S13_236V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os02g13530.1 (Oryza sativa), 3'ss of exon 1
gtgtgtgtttcattgcaacctggttcactgtgtgttgcgttgtttcggtagagttgttgtgcggtcgagtttcgggttgccccaaaaaaagagagctgagagt-cgtgtgt-tgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA
                      || |   | ||  | |      || |  ||      | ||  | | |||||  |  |||      |     |   | | ||  | ||||  |      ||||| || |||||||| |||||||| |||||||||||||| |  ||  || |   |||||| ||||||  |||| | || || |||||||| ||||||||||
----------------------gtgcgtcgcgtcctcctcctcctccggtgaccgtccgggc--tagggtttcccgccgccggcgtgaggctcatgcgtgcgtgtgcgtgtgcgtgtgtgcagGCGGATCTGAAGGAGAAGCTGGCGAAGCTGTACGAGGTGAAGGACTCCAACTGCATCTTCGTGTTCAAGTTCCGCACCCACTTCGGAGGAGGCAAGTCCA

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|37850086|gb|BJ608094.1|BJ608094
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|37825316|gb|BJ583382.1|BJ583382
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|37852779|gb|BJ610787.1|BJ610787
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|162218184|gb|FC394189.1|FC394189
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|162169907|gb|FC345847.1|FC345847
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|208387629|gb|DC953371.1|DC953371
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|67692745|gb|BJ952978.1|BJ952978
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|162218185|gb|FC394190.1|FC394190
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
EST: gi|208370058|gb|DC940365.1|DC940365
EST:     ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAG                         GCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG
genomic: ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 40

ATTATTGACGTTCTGCACCCAGGTCGTGCCAATGTCTCCAAGgtgtgtgttt ... gatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttcgggttgccccaaaaaaagagagctgagagtcgtgtgttgatcaaacagGCTGAGCTGAAGGATAAGCTGGCAAAGCTGTACGAGGTTAGAGATCCCCAGACCATCTTTGTGTTCGGGTTCAGAACGCATTTCGGAGGTGGCAAGTCCA
                                         tgttgat  putative branch site (score: 40)
                 aaaaaaaga  TA-rich tract