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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggtttatgttaagtgcatgtttgtagagagcatccgtacattggcccctgaagtatgtgacgtagcatcaggtttctgaaggttttttttgttttggatctgtgactcttatttttttcctgcgatgctcaatttgatgcatggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCTTTGGCAATGTCTTGAGTGCAAACCTTGGACAAGCTCCGGCACGGCAGGC

Basic information

species Physcomitrella patens
transcript PP1S160_44V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S160_44V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G47720.4 (Arabidopsis thaliana), 3'ss of exon 2
gtgaggtttatgttaagtgcatgtttgtagagagcatccgtacattggcccctgaagtatgtgacgtagcatcaggtttctgaaggttttttttgttttggatctgtgactcttatttttttcctgcgatgctcaatttgatgcatggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCTTTGGCAATGTCTTGAGTGCAAACCTTGGACAAGCTCCGGCACGGCAGGC
                                                                 ||||  | || | |  ||    | | | | | |    ||| ||  ||       ||| |    || |||    || | | |   ||  ||| ||  | |||||| |   ||| || ||  ||||||| |||||||| ||||||||||||||||| | ||| || ||||| ||||| || ||| | |||||
-----------------------------------------------------------------gtagt-ttagttatacgactactctctgtctctc---tctctgcttcggccaagttttc----attctcttactgtttcttctcat--agCCGCACTTAAGAGAGCACATGTTGATCCGGCCCTTGTGGAAGAGGTCTTCTTTGGCAATGTCTTAACTGCCAATCTTGGGCAAGCACCAGCAAGACAGGC

upper sequence: PP1S160_44V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ29932 (Selaginella moellendorffii), 3'ss of exon 2
gtgaggtttatgttaagtgcatgtttgtagagagcatccgtacattggcccctgaagtatgtgacgtagcatcaggtttctgaaggttttttttgttttggatctgt-gactcttatttttttcctgcgatgctcaatttgatgcatggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCTTTGGCAATGTCTTGAGTGCAAACCTTGGACAAGCTCCGGCACGGCAGGC
                                                                                                         || || | | |||  ||  |        |    | |          || || |||| |   |||  | ||  | || ||  | || ||| ||||||| |||||||||||||| ||||| || ||||| || |||||||| ||  |||||||
---------------------------------------------------------------------------------------------------------gtagaatgtcattcgttagcgcttgcattattctgggaattcttcttgtagGGGCGATCGCGAGGGCGGGGATCGATCCAGCGCTGGTTCAAGAGGTTTTCTTTGGCAATGTGTTGAGCGCCAACCTCGGCCAAGCTCCCGCCAGGCAGGC

upper sequence: PP1S160_44V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ25111 (Selaginella moellendorffii), 3'ss of exon 2
gtgaggtttatgttaagtgcatgtttgtagagagcatccgtacattggcccctgaagtatgtgacgtagcatcaggtttctgaaggttttttttgttttggatctgtgactcttatttttttcctgcgatgctcaatttgatgcatggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCTTTGGCAATGTCTTGAGTGCAAACCTTGGACAAGCTCCGGCACGGCAGGC
                                                                                                    | |         ||  ||    | |||  |  ||   | |          || || |||| |   |||  | ||  | || ||  | || ||| ||||||| |||||||||||||| ||||| || ||||| || |||||||| ||  |||||  
----------------------------------------------------------------------------------------------------ggtagaatgtcattcgttagcgcttgcattattc---tgggaattcttcttgtAGGGGCGATCGCGAGGGCGGGGATCGATCCAGCGCTGGTTCAAGAGGTTTTCTTTGGCAATGTGTTGAGCGCCAACCTCGGCCAAGCTCCCGCCAGGCAG--

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|67718754|gb|BJ969013.1|BJ969013
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|18358109|gb|BJ190168.1|BJ190168
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|162258773|gb|FC434572.1|FC434572
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100445895|gb|CJ970194.1|CJ970194
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGCTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|18325088|gb|BJ157084.1|BJ157084
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100421800|gb|BY993649.1|BY993649
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|18331714|gb|BJ163725.1|BJ163725
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|18360796|gb|BJ192859.1|BJ192859
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|18349630|gb|BJ181680.1|BJ181680
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208389079|gb|DC937412.1|DC937412
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208400031|gb|DC908608.1|DC908608
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100364678|gb|BY947854.1|BY947854
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208390080|gb|DC942381.1|DC942381
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100387301|gb|BY970445.1|BY970445
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|162156306|gb|FC332330.1|FC332330
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208391223|gb|DC933512.1|DC933512
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|40781593|gb|AJ583523.1|AJ583523
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|18345885|gb|BJ177928.1|BJ177928
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208367731|gb|DC940202.1|DC940202
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100432533|gb|BY960504.1|BY960504
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208369407|gb|DC936096.1|DC936096
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208358809|gb|DC935195.1|DC935195
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100448720|gb|CJ973019.1|CJ973019
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|100386211|gb|BY987878.1|BY987878
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
EST: gi|208358457|gb|DC930589.1|DC930589
EST:     CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAG                         CGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT
genomic: CTCTCTGTCTAGCCTGTCGGCAACCAAGCTGGGGTCCACTGCGATTCAAGgtgaggttta ... tggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgtgactcttatttttttcctgcgatgctcaatttgatgcatggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCTTTGGCAATGTCTTGAGTGCAAACCTTGGACAAGCTCCGGCACGGCAGGC
                                   atttgat  putative branch site (score: 5)
        actcttattttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggtttatgttaagtgcatgtttgtagagagcatccgtacattggcccctgaagtatgtgacgtagcatcaggtttctgaaggttttttttgttttggatctgtgactcttatttttttcctgcgatgctcaatttgatgcatggaatgcagCGGCGGTGAAGAGATCTGGTGTGGACCCTTCCCTTGTTGAAGAGGTGTTCTTTGGCAATGTCTTGAGTGCAAACCTTGGACAAGCTCCGGCACGGCAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT