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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcagcgtcttgaattggtgcatttaggaaatccaggattactgcagcgtggttctcgcactgctgtgtttgttccctcatcgtattctcgcgaggtgctcatgaagtgaatttgtgtatttggctgaaattcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAG

Basic information

species Physcomitrella patens
transcript PP1S168_70V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S168_70V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 12
gttggttcagcgtcttgaattggtgcatttaggaaatccaggattactgcagcgtggttctcgcactgctgtgtttgttccctcatcgtattc-tcgcgaggtgctcatgaagtgaatttgtgtatttggctgaaattcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAG
                                                     || | | ||  | ||    | || |  |    |  ||||| | || |     | |   |||  |||  | || |      | |||      |||| |||||||| ||||| |||||||| || || |||||||| || ||||||||||| ||||| ||||| ||||||||||| |
-----------------------------------------------------gtagatgtc--attgtgaagcttttctctagcttctattcattgcaatcacgtaacatagtctattgctctaatacttctatattt----tagGTTCCAACAGGCTGGAAATTCTTTGGCAATCTAATGGATGCTGGGATGTGCTCTGTATGCGGAGAAGAAAGTTTTGGAACCG

upper sequence: PP1S168_70V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
gttggttcagcgtcttgaattggtgcatttaggaaatccaggattactgcagcgtggttctcgcactgctgtgtttgttccctcatcgtattctcgcgaggtgctcatgaagtgaatttgtgtatttggctgaaattcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAG
                                                     ||   | || |  |||    | | | |     |  | |||||   |      ||| |  | | ||  | | | |   | ||   |    ||||| |||||||| |||||||| |||||||| || |||||||| || ||||| ||||| || || ||||| ||||||||||| |
-----------------------------------------------------gtacatgtcaccgtgcaacttctatccagc--ttcttttctcctaac---tacataatttaatttcatatctcta-ttaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
















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|100417708|gb|BY975615.1|BY975615
EST:     CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAG                         GTAC-AACAGGGTGGAAGTTCTTTGGTAAC
genomic: CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAGgttggttcag ... ttcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAAC
EST: gi|162259444|gb|FC434955.1|FC434955
EST:     CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAG                         GTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGC
genomic: CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAGgttggttcag ... ttcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGC
EST: gi|162189353|gb|FC366511.1|FC366511
EST:     CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAG                         GTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGC
genomic: CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAGgttggttcag ... ttcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGC
EST: gi|162169785|gb|FC345322.1|FC345322
EST:     CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAG                         GTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGC
genomic: CCGCTGCGCTTGATGTGGTGGCTAAGAAGTTGAACCTTAAGTTTTTCGAGgttggttcag ... ttcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgcgaggtgctcatgaagtgaatttgtgtatttggctgaaattcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAG
                      tgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcagcgtcttgaattggtgcatttaggaaatccaggattactgcagcgtggttctcgcactgctgtgtttgttccctcatcgtattctcgcgaggtgctcatgaagtgaatttgtgtatttggctgaaattcgctacagGTACCAACAGGGTGGAAGTTCTTTGGTAACCTCATGGATGCCGGCATGTGCTCTGTGTGCGGTGAAGAGAGTTTTGGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA