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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcatataagcacatgtacctctctgctgaagttgaagaacatgatttgggaagacttgtattatacgcaataacttagacgtaaggcatgcattctctagatattttctgagtaagcgattgctaccactgctgcacaaggtataacatttcttttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTCGGCCATGAGGTGGACCTCCTACATTTTGAAATAAACCAGGCGATTCCTG

Basic information

species Physcomitrella patens
transcript PP1S99_189V6.2
intron # 3
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|18361734|gb|BJ193801.1|BJ193801
EST:     CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAAT                         ATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
genomic: CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAATgtatgttcat ... ttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
EST: gi|100404339|gb|BY973527.1|BY973527
EST:     CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAAT                         ATGGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTT
genomic: CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAATgtatgttcat ... ttgtctacagATGGG-CGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTT
EST: gi|100387720|gb|BY951720.1|BY951720
EST:     CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAAT                         ATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
genomic: CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAATgtatgttcat ... ttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
EST: gi|208347039|gb|DC909337.1|DC909337
EST:     CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAAT                         ATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
genomic: CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAATgtatgttcat ... ttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
EST: gi|100362233|gb|BY947256.1|BY947256
EST:     CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAAT                         ATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC
genomic: CAGCAATATCTCTGATGTTCCCAGTTGGAGACGATGCTACCTATCATAATgtatgttcat ... ttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtaagcgattgctaccactgctgcacaaggtataacatttcttttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTCGGCCATGAGGTGGACCTCCTACATTTTGAAATAAACCAGGCGATTCCTG
                               gtataac  putative branch site (score: 3)
                                     catttcttttgtct  CT-rich tract
                                tataacatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcatataagcacatgtacctctctgctgaagttgaagaacatgatttgggaagacttgtattatacgcaataacttagacgtaaggcatgcattctctagatattttctgagtaagcgattgctaccactgctgcacaaggtataacatttcttttgtctacagATGGGCGGGTGTCCAGAGGCCTCTACAACTTGCAATGCCACAAGCTGCTTCGGCCATGAGGTGGACCTCCTACATTTTGAAATAAACCAGGCGATTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA