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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCACTGCGGATCATGCTGGGCTTTTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtacccttaattaagttagtgtactaggaatttgaagtgcgtgtctgtatgcaattgtgtgtttcattcttgtatttaggttcttctggacaattgcttcgcagggctgcctttcattggtttcgagttttctttttttctcatgatttttatatttgttaaatgttttgctttcaatcttggatgttgcag

Basic information

species Physcomitrella patens
transcript PP1S7_406V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S7_406V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ32889 (Selaginella moellendorffii), 5'ss of exon 5
GGTCACTGCGGATCATGCTGGGCTTTTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtacccttaattaagttagtgtactaggaatttgaagtgcgtgtctgtatgcaattgtgtgtttcattcttgtatttaggttcttctggacaattgcttcgcagggctgcctttcattggtttcgagttttctttttttctcatgatttttatatttgttaaatgttttgctttcaatcttggatgttgcag
|||||||| || ||||||||||||||||| ||||| ||| ||||||| ||||| || ||||| | |   ||||||||||||      |||    ||  | |  |     | || | || |  |    ||||  | |  | | |||                                                                                                                              
GGTCACTGTGGGTCATGCTGGGCTTTTGGAGCTGTCGAGGCACTGACGGATCGATTTTGCATCCTCAACAATGAAgtgagtgga--gaatct--tttcttttttgttcgtgtgcattgtg-atacagatgct-tcgcttttctcag-----------------------------------------------------------------------------------------------------------------------------

upper sequence: PP1S7_406V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ05715 (Selaginella moellendorffii), 5'ss of exon 5
GGTCACTGCGGATCATGCTGGGCTTTTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtacccttaattaagttagtgtactaggaatttgaagtgcgtgtctgtatgcaattgtgtgtttcattcttgtatttaggttcttctggacaattgcttcgcagggctgcctttcattggtttcgagttttctttttttctcatgatttttatatttgttaaatgttttgctttcaatcttggatgttgcag
|||||||| || ||||||||||||||||| ||||| ||| ||||||| ||||| || ||||| | |   ||||||||||||            |  | | |  |     |||   || |||||   |    |      || |||  | ||    | ||                                                                                                                 
GGTCACTGTGGGTCATGCTGGGCTTTTGGAGCTGTCGAGGCACTGACAGATCGATTTTGCATCCTCAACAATGAAgtgagtg-----------gagaatcttttc----tttctcgttcgtgtgcattgtgacacagatgcttcgctttt---ctcag-----------------------------------------------------------------------------------------------------------------
















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|208400722|gb|DC904900.1|DC904900
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|67570161|gb|BJ942985.1|BJ942985
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTG
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTG
EST: gi|162171829|gb|FC348979.1|FC348979
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|208377375|gb|DC906644.1|DC906644
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|162195749|gb|FC371140.1|FC371140
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|100425949|gb|BY977201.1|BY977201
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|100371973|gb|BY967643.1|BY967643
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|162162644|gb|FC338946.1|FC338946
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|208397325|gb|DC908229.1|DC908229
EST:     TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
genomic: TTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTCGAGTGC
EST: gi|18373041|gb|BJ204643.1|BJ204643
EST:     TGGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAA                         AGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATTTCGAGTG
genomic: TGGGG-CTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtaccc ... gatgttgcagAGTGTGTCACTATCAGAGAACGATCTCTTAGCATGCTGTGGATT-CGAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTCACTGCGGATCATGCTGGGCTTTTGGGGCTGTTGAGTCACTGACTGATCGTTTCTGCATTCACTTGAATGAAgtgagtacccttaattaagttagtgtactaggaatttgaagtgcgtgtctgtatgcaattgtgtgtttcattcttgtatttaggttcttctggacaattgcttcgcagggctgcctttcattggtttcgagttttctttttttctcatgatttttatatttgttaaatgttttgctttcaatcttggatgttgcag

- - - - - - - - - - - - - - - GCTGTT