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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacctcaattcttgcggaaagacgtgggttttacgggttttagggttggagggtgcatttagggctccactcagcatgggagcatgggaatggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTGTAGCAACAGCTTGTCTGACGGTGTTCATAGGATGTCATCGGTCTGTGAA

Basic information

species Physcomitrella patens
transcript PP1S47_5V6.1
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|18357303|gb|BJ189362.1|BJ189362
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18357467|gb|BJ189526.1|BJ189526
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18344957|gb|BJ176998.1|BJ176998
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|100431216|gb|BY960085.1|BY960085
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18356652|gb|BJ188711.1|BJ188711
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|100388316|gb|BY951918.1|BY951918
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|100423679|gb|BY976504.1|BY976504
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|208389036|gb|DC937369.1|DC937369
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|67704224|gb|BJ964457.1|BJ964457
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCA
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCA
EST: gi|67572635|gb|BJ945459.1|BJ945459
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18343415|gb|BJ175453.1|BJ175453
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|162211220|gb|FC386932.1|FC386932
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|100368970|gb|BY984964.1|BY984964
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18358244|gb|BJ190303.1|BJ190303
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|162242981|gb|FC417621.1|FC417621
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18375136|gb|BJ206714.1|BJ206714
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
EST: gi|18368931|gb|BJ201016.1|BJ201016
EST:     GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAG                         GTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG
genomic: GAGCAGTCGGGCAGGCATGGCGGAGAAGGTGGCCAGTGCCGCCCTGATAGgtattttcgt ... tggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggagggtgcatttagggctccactcagcatgggagcatgggaatggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTGTAGCAACAGCTTGTCTGACGGTGTTCATAGGATGTCATCGGTCTGTGAA
           attta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacctcaattcttgcggaaagacgtgggttttacgggttttagggttggagggtgcatttagggctccactcagcatgggagcatgggaatggttggcagGTTTGACGTTGATGCCTCTGGTGGTGAAGGTGAATCCCAATTTCAACGTTGTAGCAACAGCTTGTCTGACGGTGTTCATAGGATGTCATCGGTCTGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG