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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTACAAGGCAAGAGATGTTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctgacagtaatttattttttctccaatctgaagataactcgtgtgtaagatgaaatgatgaattcgctgcaattgagtatcgtaattttatcca...

Basic information

species Physcomitrella patens
transcript PP1S219_94V6.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S219_94V6.4 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os06g49110.2 (Oryza sativa), 5'ss of exon 4
GTGTACAAGGCAAGAGATGTTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtc--tgacagtaatttattttttctccaatctgaa--gataactcgtgtgtaagatgaaatgatgaattcgctgcaattgagtatcgtaattttatcca
|| |||||| |  | ||||||||||| |||||| |||| || ||||| ||||| ||||||||  ||||||||  ||   ||   ||||| ||||| | |   || || |   ||| || | || | |  | | |   |   ||| || ||                       
GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaacgaatataattcattttctgtttcatgtgtattaatatcttgagt-tgacttaatactctttgttc-cttcag----------------------
















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|162250292|gb|FC425946.1|FC425946
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162166620|gb|FC343512.1|FC343512
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|100384135|gb|BY950521.1|BY950521
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162190655|gb|FC367541.1|FC367541
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162154906|gb|FC331948.1|FC331948
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162186428|gb|FC362984.1|FC362984
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162166262|gb|FC342855.1|FC342855
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162150373|gb|FC326645.1|FC326645
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162157382|gb|FC333484.1|FC333484
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162179122|gb|FC355587.1|FC355587
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|208394292|gb|DC904112.1|DC904112
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGANGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162150767|gb|FC327039.1|FC327039
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162177008|gb|FC353685.1|FC353685
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162270868|gb|FC446897.1|FC446897
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
EST: gi|162156546|gb|FC332154.1|FC332154
EST:     TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAG                         TCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC
genomic: TTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctga ... atacctgcagTCTTCAACTGGAGATGAGGCTTACAATCCTGATGGGCTGGTGCCACGGTGC

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTACAAGGCAAGAGATGTTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtctgacagtaatttattttttctccaatctgaagataactcgtgtgtaagatgaaatgatgaattcgctgcaattgagtatcgtaattttatcca

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