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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcaaagtcatttcaacttatgctcaatttaggaacgattttcatcatactgaattcacttcgaccacttttatactctgcattcctgtcgagtcatatttcagaattccttattcattttgaagtcggaggttccattcgaaaaattctgacttaggtccctttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCTTAGACAGATCTTCAACGGTGTGTTCATGAAGGTGAACAAGGCCACTGTG

Basic information

species Physcomitrella patens
transcript PP1S163_37V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S163_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20182 (Selaginella moellendorffii), 3'ss of exon 3
gttagttcaaagtcatttcaacttatgctcaatttaggaacgattttcatcatactgaattcacttcgaccacttttatactctgcattcctgtcgagtcatatttcagaattccttattcattttgaagtcggaggttccattcgaaaaattctgact--taggtccctttcgattcag-
                                                                                                                     |||| || ||||  | | | ||        |    |||||||   | || | ||    |  ||    |||| |   ||  |   ||||| |  |||     ||| |  |  |       |      |  | | ||  ||   | | ||                 
-----------------------------------------------------------------------------------------------------------------gtaaattccttgtgaaagctgcgattgtgaaacgagttctctgactatcacgttctttcttttatagATCTTCAATGGGGTGTTCATGAAGGTGAACAAG-----GCAACCATGAACATGCTCAAGAGAGTCGAGCCGTACGTGACTTACGG-----------------

upper sequence: PP1S163_37V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ23123 (Selaginella moellendorffii), 3'ss of exon 3
gttagttcaaagtcatttcaacttatgctcaatttaggaacgattttcatcatactgaattcacttcgaccacttttatactctgcattcctgtcgagtcatatttcagaattccttattcattttgaagtcggaggttccattcgaaaaattctgacttaggtccctttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCTTAGACAGATCTTCAACGGTGTGTTCATGAAGGTGAACAAGGCCACTGTG
                                                                                                             |||||||| |  |  |||   | |  | | | | |      | | | || |   | | |||  ||  |   |||| |   ||  |   ||||| |  |||     ||| |  |  |       |      |  | | ||  ||   | | ||                 
----------------------------------------------------------------------------------------------------------gtaaattccttgtgaaagttgcgattgt-gatacgagttctcttactatcacattctttctttt--atagATCTTCAATGGGGTGTTCATGAAGGTGAACAAG-----GCAACCATGAACATGCTCAAGAGAGTCGAGCCGTACGTGACTTACGG-----------------
















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|67570858|gb|BJ943682.1|BJ943682
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67724620|gb|BJ974879.1|BJ974879
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67717640|gb|BJ967899.1|BJ967899
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|162280069|gb|FC456463.1|FC456463
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67692080|gb|BJ952313.1|BJ952313
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67712911|gb|BJ966360.1|BJ966360
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|162280068|gb|FC456462.1|FC456462
EST:     TTTTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTGGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67578517|gb|BJ950684.1|BJ950684
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67568873|gb|BJ941697.1|BJ941697
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67726154|gb|BJ976413.1|BJ976413
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
EST: gi|67694157|gb|BJ954390.1|BJ954390
EST:     TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGG                         TATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT
genomic: TTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCT

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: 31 (upstream exon), 35 (downstream exon)
Score: 72

GAGAAGGAAATTATTAGTTTGAAGAGGGAGGCTAAGCTCAAGGGTGGATTCTATGTCGAGCCAGAACCTAAACTTATGTTTGTCATTCGAATCCGTGGgttagttcaa ... ttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCTTAGACAGATCTTCAACGGTGTGTTCATGAAGGTGAACAAGGCCACTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaagtcggaggttccattcgaaaaattctgacttaggtccctttcgattcagTATCAACGACATGCACCCCAAGGTTAGAAAGATCATGCAGCTGTTGAGGCTTAGACAGATCTTCAACGGTGTGTTCATGAAGGTGAACAAGGCCACTGTG
                            ttctgac  putative branch site (score: 72)
                                        tccctttc  putative PPT
                       aaaaattct  TA-rich tract