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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgatcaatgatcgttgcacagtcacaattctctcttttgaagcaaggcttcccacgcaatgaacgcctactttgcatgcccatgtggctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAAGGAGGATTTCAGAACAATTCTGTTGCAACTGCAGCGATTCTCGAGGCGA

Basic information

species Physcomitrella patens
transcript PP1S63_71V6.1
intron # 2
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|208346899|gb|DC913110.1|DC913110
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162224299|gb|FC399532.1|FC399532
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208344950|gb|DC909061.1|DC909061
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208355071|gb|DC926722.1|DC926722
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|100388447|gb|BY952049.1|BY952049
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208366640|gb|DC955660.1|DC955660
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCTGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208376695|gb|DC914518.1|DC914518
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208379343|gb|DC922929.1|DC922929
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162215165|gb|FC390777.1|FC390777
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208355548|gb|DC942668.1|DC942668
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCTGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208345321|gb|DC912952.1|DC912952
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAN                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162224298|gb|FC399531.1|FC399531
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162211136|gb|FC387160.1|FC387160
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162274840|gb|FC451075.1|FC451075
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162211135|gb|FC387159.1|FC387159
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208383281|gb|DC928267.1|DC928267
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|208356863|gb|DC926874.1|DC926874
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
EST: gi|162274839|gb|FC451074.1|FC451074
EST:     GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAG                         GTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA
genomic: GTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAA

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: 27 (upstream exon), 30 (downstream exon)
Score: 3

AGATAACTTCGACGCTACCAACAATCTGTTTGTGTCTATTACCCCCGCCAGTAAGGGCAGCATAACAGAATATGGATCTCCAGAGAAGTTTTTGGATGAGgtgggctctc ... ctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAAGGAGGATTTCAGAACAATTCTGTTGCAACTGCAGCGATTCTCGAGGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaggcttcccacgcaatgaacgcctactttgcatgcccatgtggctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAAGGAGGATTTCAGAACAATTCTGTTGCAACTGCAGCGATTCTCGAGGCGA
                                           ggctgat  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgatcaatgatcgttgcacagtcacaattctctcttttgaagcaaggcttcccacgcaatgaacgcctactttgcatgcccatgtggctgattgcagGTCTCCTATCTGTTCGGGAAGCAAGCCTACAATGGCAAGACTGCATCCGAAGGAGGATTTCAGAACAATTCTGTTGCAACTGCAGCGATTCTCGAGGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - ttgcaca