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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtctccatttctatctgtgtagacctcgtatctggattgcctagaaacttgggacttgcagactcttacttcgataaaatttgttagtttcttataatccgttgcattactgaagtttgatcatgtaatattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATAGACTGCTTCGTCCAGACGTTTAAGAATGAC

Basic information

species Physcomitrella patens
transcript PP1S15_443V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S15_443V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT3G54110.1 (Arabidopsis thaliana), 3'ss of exon 6
gttagtgtctccatttctatctgtgtagacctcgtatctggattgcctagaaacttgggacttgcagactcttacttcgataaaatttgttagtttcttataatccgttgcattactga--agtttgatcatgtaatattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATAGACTGCTTCGTCCAGACGTTTAAGAATGAC
                                                          |    | |    || |   |  | ||  |||  ||||| ||  |   |||| | | | ||   | ||  ||| |||  | | |  ||||| ||||| |||||||||||||        ||||||||||||||||| || |||||||||||| | ||  | ||||  |||
----------------------------------------------------------gtaaagtatttactcatgacattgaaccttg--agtttatt-caccacgtttcctgattgtctacttaaatcttgttgtgtgg--cagGTTAAGTCAAGAATGATGGGAGAT---TCTGGTGCTTACAAGGGCACCATTGACTGCTTCGTCAAAACTCTGAAGAGCGAC
















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|18334877|gb|BJ166894.1|BJ166894
EST:     GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTG                         GTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
genomic: GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
EST: gi|208396055|gb|DC924521.1|DC924521
EST:     GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTNGATGTG                         GTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
genomic: GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
EST: gi|162262932|gb|FC439299.1|FC439299
EST:     GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTG                         GTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
genomic: GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
EST: gi|162268960|gb|FC445764.1|FC445764
EST:     GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTG                         GTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
genomic: GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
EST: gi|37833787|gb|BJ591799.1|BJ591799
EST:     GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTG                         GTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
genomic: GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
EST: gi|162262931|gb|FC439298.1|FC439298
EST:     GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTG                         GTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA
genomic: GATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATA

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: 23 (upstream exon), 33 (downstream exon)
Score: 4

GTTAAAGCTCCCTGGCTTTACAGACAACGTTGTTACGCACATCCTCTCCGGATTGGGAGCTGGCTTTATTGCTGTTTGCGTTGGCTCTCCTGTTGATGTGgttagtgtct ... tattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATAGACTGCTTCGTCCAGACGTTTAAGAATGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtttcttataatccgttgcattactgaagtttgatcatgtaatattgtccagGTGAAGTCTAGAATGATGGGAGGAGGGCAGGGTGCTTACAAGGGCACAATAGACTGCTTCGTCCAGACGTTTAAGAATGAC
                               gtttgat  putative branch site (score: 4)
     ttcttataat  TA-rich tract