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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattagagcgatgaaaagcataatctagaaactcagtaacgagagacgatagttgttgtaaaggttcattttcatatactacatcgggttgtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTGAAGTTACCATCAATTTGGATGGAACCGGAATATGTGATTGCGACACTGG

Basic information

species Physcomitrella patens
transcript PP1S37_83V6.1
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|162196840|gb|FC373895.1|FC373895
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162222109|gb|FC397337.1|FC397337
EST:     GGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162196839|gb|FC373894.1|FC373894
EST:     ACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: ACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|208369522|gb|DC936312.1|DC936312
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162189059|gb|FC365177.1|FC365177
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|18337884|gb|BJ169908.1|BJ169908
EST:     CCGCGACTACCAATGGCGTTGCGNCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: CCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162222108|gb|FC397336.1|FC397336
EST:     GGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162153155|gb|FC329561.1|FC329561
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|208361844|gb|DC950116.1|DC950116
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162208762|gb|FC384898.1|FC384898
EST:     CGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: CGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162208763|gb|FC384899.1|FC384899
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|37838754|gb|BJ596762.1|BJ596762
EST:     GGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162271020|gb|FC447425.1|FC447425
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162150420|gb|FC326692.1|FC326692
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
EST: gi|162150421|gb|FC326693.1|FC326693
EST:     GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAG                         AGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG
genomic: GGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTG

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: 28 (upstream exon), 22 (downstream exon)
Score: 9

GAGCGGAGGTTAACTACTTCGCGGCATGGAGTGCGTAGGGTTGTGGTCCGGGGTTCCACCGCGACTACCAATGGCGTTGCGGCTGATGTTGTCGAAGGAGgtgcgtgatg ... gtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTGAAGTTACCATCAATTTGGATGGAACCGGAATATGTGATTGCGACACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgatagttgttgtaaaggttcattttcatatactacatcgggttgtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTGAAGTTACCATCAATTTGGATGGAACCGGAATATGTGATTGCGACACTGG
                   ttcattttcatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattagagcgatgaaaagcataatctagaaactcagtaacgagagacgatagttgttgtaaaggttcattttcatatactacatcgggttgtgcttgcagAGAGTGCACGTGTAGGATCTGTTTCGAGAGAAACCAAAGAGACGAGTGTTGAAGTTACCATCAATTTGGATGGAACCGGAATATGTGATTGCGACACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA