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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagcctttccttcgcacatgtttctttaactatgtagtagtggttactgttctgattcattttttcctgtagtggtttgttgatatctatgctgcttcaccagttatacgatttacggttttttcctctctaacttttcgattgatctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTACGTCTCTTACTCAAAT

Basic information

species Physcomitrella patens
transcript PP1S204_22V6.1
intron # 4
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|100389909|gb|BY971261.1|BY971261
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
EST: gi|18328336|gb|BJ160340.1|BJ160340
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
EST: gi|18327270|gb|BJ159272.1|BJ159272
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAA
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAA
EST: gi|18329206|gb|BJ161212.1|BJ161212
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
EST: gi|18374970|gb|BJ206548.1|BJ206548
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAA
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAA
EST: gi|100396548|gb|BY990180.1|BY990180
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
EST: gi|18343567|gb|BJ175605.1|BJ175605
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
EST: gi|18329759|gb|BJ161765.1|BJ161765
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAA
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAA
EST: gi|18358397|gb|BJ190456.1|BJ190456
EST:     AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTT                         TGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC
genomic: AATTTTAATCCTTCGTACTTTCAAAACGCTTTTAAAAAGCTTCGAATTTTgtaagagcct ... ctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatacgatttacggttttttcctctctaacttttcgattgatctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTACGTCTCTTACTCAAAT
                                            tctgctttc  CT-rich tract
                             taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagcctttccttcgcacatgtttctttaactatgtagtagtggttactgttctgattcattttttcctgtagtggtttgttgatatctatgctgcttcaccagttatacgatttacggttttttcctctctaacttttcgattgatctgctttcagTGATGCTAGTAACAACAACATCGAAGGAAATATTCCTCAACAGTTTCCTACGTCTCTTACTCAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA