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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtccccccaaaacagtaattagtgttccattcgttgtctgacctagatatgccgggtaaaacctgatctgatcctgctgcatcgttggtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGATATTCATGACTTTTTCTCATTTTCTGGAGAGATTGAGAATATTGAGCTTC

Basic information

species Physcomitrella patens
transcript PP1S9_32V6.1
intron # 1
splice site 3'
intron type U2

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|100378310|gb|BY949787.1|BY949787
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208359261|gb|DC939070.1|DC939070
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|18342157|gb|BJ174192.1|BJ174192
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208373441|gb|DC941052.1|DC941052
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100358635|gb|BY965746.1|BY965746
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100387784|gb|BY970529.1|BY970529
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208368227|gb|DC931453.1|DC931453
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100388020|gb|BY988493.1|BY988493
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162265878|gb|FC442465.1|FC442465
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208357096|gb|DC942730.1|DC942730
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208393431|gb|DC942515.1|DC942515
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208396861|gb|DC908181.1|DC908181
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162265877|gb|FC442464.1|FC442464
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100397943|gb|BY954009.1|BY954009
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162280268|gb|FC456285.1|FC456285
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208387672|gb|DC937237.1|DC937237
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100444933|gb|BY982761.1|BY982761
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162240163|gb|FC418290.1|FC418290
EST:     TTCATCAATCGAGAAGGAGAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208384457|gb|DC911543.1|DC911543
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100405823|gb|BY973872.1|BY973872
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100417073|gb|BY957153.1|BY957153
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162230915|gb|FC406754.1|FC406754
EST:     TTCATCAATCGAGAAGGAGAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162240162|gb|FC418289.1|FC418289
EST:     CGAGAAGGAGAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: CGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100374498|gb|BY985807.1|BY985807
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208400060|gb|DC908623.1|DC908623
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162280269|gb|FC456286.1|FC456286
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100437426|gb|BY961512.1|BY961512
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208391737|gb|DC937955.1|DC937955
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100399961|gb|BY990708.1|BY990708
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|162230914|gb|FC406753.1|FC406753
EST:     TTCATCAATCGAGAAGGAGAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|208375442|gb|DC940496.1|DC940496
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100449088|gb|CJ973387.1|CJ973387
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100385442|gb|BY969779.1|BY969779
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
EST: gi|100436109|gb|BY979384.1|BY979384
EST:     TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACG                         ACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT
genomic: TTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGAT

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: 33 (upstream exon), 31 (downstream exon)
Score: 16

TAGGAATCGGCGACAGTTTCGTGGTTTGATTGGTCTATTTCGACTAGGGTTTCATCAATCGAGAAGGAAAGAGATTCCGGATCTCGCTTCAGCAATGACGgtattatgat ... gtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGATATTCATGACTTTTTCTCATTTTCTGGAGAGATTGAGAATATTGAGCTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagatatgccgggtaaaacctgatctgatcctgctgcatcgttggtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGATATTCATGACTTTTTCTCATTTTCTGGAGAGATTGAGAATATTGAGCTTC
                       atctgat  putative branch site (score: 16)
              taaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgtccccccaaaacagtaattagtgttccattcgttgtctgacctagatatgccgggtaaaacctgatctgatcctgctgcatcgttggtgtttgcagACGAACACCGTACGGGTGACCAATGTCTCAGTGAAAGCTACTGCACACGATATTCATGACTTTTTCTCATTTTCTGGAGAGATTGAGAATATTGAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT