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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccacaacattcttccttcctatttgcttgtgatagttgttactaccgcaccaattcgatataatgaaatggtgatattaatgacgttaagtgct...

Basic information

species Physcomitrella patens
transcript PP1S117_137V6.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S117_137V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G13320.1 (Arabidopsis thaliana), 5'ss of exon 12
GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccacaacattc-ttccttcctatttgctt-gtgatagttgttactaccgcaccaat-tcgatataatgaaatggtgatattaatgacgttaagtgct-----------------------
 ||||||||||||||||||||||| ||||||||| | |||||| | ||||| ||||| ||     | || |||  |||   ||  ||   ||  |   |    |  | || |  |  | || ||  |   ||   || | | |||    |  |  ||    | || || |                       
AGTTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCGgttagtatacattctttgttggctctcacaagtaaagaaacagcttatgattccacattatcctcctcatcagggaatctaaacgtccatatattcaaatgttttcatttttgttggttgtgaaag

upper sequence: PP1S117_137V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 5'ss of exon 12
GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccacaa-cattcttccttcctatttgctt-gtgatagttgttactaccgcaccaat-tcgatataatgaaatggtgatattaatgacgttaagtgct-----------------------
  |||||||||||||||||||||| ||||||||| | |||||| | ||||| ||||| ||     | || |||  |||  | || ||   ||  |   |    |  | || |  |  | || ||  |   ||   || | | |||    |  |  ||    | || || |                       
--TTCCAAACATCAAATTTAACGTGGCCAAAATGATGCAATCTCTCATTCCGATAGTCGACCAAGCGgttagtatacattctttgttggctctcacaagtaaagaaacagcttatgattccacattatcctcctcatcagggaatctaaacgtccatatattcaaatgttttcatttttgttggttgtgaaag
















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|37837109|gb|BJ595117.1|BJ595117
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|208369319|gb|DC955864.1|DC955864
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37847718|gb|BJ605726.1|BJ605726
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37821945|gb|BJ580011.1|BJ580011
EST:     AACGTCGCCAAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: AACGTCGCC-AAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162248181|gb|FC422513.1|FC422513
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|18337201|gb|BJ169225.1|BJ169225
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37828121|gb|BJ586133.1|BJ586133
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|67726258|gb|BJ976517.1|BJ976517
EST:     TTAATGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAGTCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162199120|gb|FC374590.1|FC374590
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|37826062|gb|BJ584074.1|BJ584074
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162198994|gb|FC374542.1|FC374542
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
EST: gi|162248182|gb|FC422514.1|FC422514
EST:     TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACA                         GTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT
genomic: TTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCT

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: 35 (upstream exon), 34 (downstream exon)
Score: 9

GGTTCCAAACATCAAATTTAACGTCGCCAAAATGCTCCAATCTATGATTCCTATAGTTGAATCCACAgtaagtccac ... atacttgcagGTTGTGGAGCAAACAATTCGGCCATGCTTGTTGGAACTTCAGGAAGACCCTGATGTGGATGTTCGGTTTTTCGCTGGGCAGGCCCTACAAGCCTGTGACC




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