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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctatccgggttcgttgtagggtgttatctaaagcattaatcaatggtattatcctatcgaggttctatccattgctaatagtacgtcaattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAAGGGGGAAGCCAAAGATGGTAACGGAAACTCTTTGGCGAAAGTCTCGGGC

Basic information

species Physcomitrella patens
transcript PP1S78_210V6.1
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|100406464|gb|BY955639.1|BY955639
EST:     CAAACTACAGACGTTGAAAGTGTCGCCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|162249724|gb|FC428164.1|FC428164
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|162199765|gb|FC375838.1|FC375838
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|162208443|gb|FC384198.1|FC384198
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|100447463|gb|CJ971762.1|CJ971762
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|100448830|gb|CJ973129.1|CJ973129
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|100396246|gb|BY972307.1|BY972307
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|100353533|gb|BY964854.1|BY964854
EST:     CAAACTACAGACGTTGAAAGTGTCACGGGGGATGCCTACGTAAACATCAG                         AAAAGGAA-GATCATTCCTGGGTTATGAAATTGCTATACGAGCTGCTTGGG
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGG-TTATGAAATTGCTATACGAGCTGCTTGGA
EST: gi|208383574|gb|DC903531.1|DC903531
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|100447741|gb|CJ972040.1|CJ972040
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|100452904|gb|CJ975501.1|CJ975501
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
EST: gi|18368755|gb|BJ200840.1|BJ200840
EST:     CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAG                         AAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA
genomic: CAAACTACAGACGTTGAAAGTGTCACCGGGGATGCCTACGTAAACATCAGgtcggaacca ... aattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtattatcctatcgaggttctatccattgctaatagtacgtcaattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAAGGGGGAAGCCAAAGATGGTAACGGAAACTCTTTGGCGAAAGTCTCGGGC
                              tgctaat  putative branch site (score: 2)
                                 taatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctatccgggttcgttgtagggtgttatctaaagcattaatcaatggtattatcctatcgaggttctatccattgctaatagtacgtcaattttgcagAAAAGGAAAGATCATTCCTGGTTATGAAATTGCTATACGAGCTGCTTGGAAGGGGGAAGCCAAAGATGGTAACGGAAACTCTTTGGCGAAAGTCTCGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG