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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcatttttcacctgcttcagctggctacatatttttcgtattcccacgggctttttgacaaaaacctatttgactgcgtttactgttcacattcagagcggttttttttttttttttttttttttttttttgtgatgtatagacttctgtgcaagcggctattactgacggtgaggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGACAGTATTGGAGATTCATGTTGAATATGACCGTGAAAAGCGCACCAAGCCG

Basic information

species Physcomitrella patens
transcript PP1S43_166V6.1
intron # 20
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|37852255|gb|BJ610263.1|BJ610263
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|162222919|gb|FC399381.1|FC399381
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|37842145|gb|BJ600153.1|BJ600153
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|100390331|gb|BY952739.1|BY952739
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGGATGACAAGA
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGG-ATGACAAGA
EST: gi|37836849|gb|BJ594857.1|BJ594857
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|162184430|gb|FC359176.1|FC359176
EST:     ACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: ACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|162254784|gb|FC430761.1|FC430761
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|37828726|gb|BJ586738.1|BJ586738
EST:     GACTNTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|162255906|gb|FC431982.1|FC431982
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|67697565|gb|BJ957798.1|BJ957798
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|37841870|gb|BJ599878.1|BJ599878
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
EST: gi|162255907|gb|FC431983.1|FC431983
EST:     GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAG                         GTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC
genomic: GACTCTAAAGACTACTATGGGCTTGCACCAGGCAAAAGCGTGATCCTTAGgttagtcatt ... ggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgatgtatagacttctgtgcaagcggctattactgacggtgaggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGACAGTATTGGAGATTCATGTTGAATATGACCGTGAAAAGCGCACCAAGCCG
                                 tactgac  putative branch site (score: 1)
     atgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcatttttcacctgcttcagctggctacatatttttcgtattcccacgggctttttgacaaaaacctatttgactgcgtttactgttcacattcagagcggttttttttttttttttttttttttttttttgtgatgtatagacttctgtgcaagcggctattactgacggtgaggtctgacagGTGGGCATATCCGGTCAAATGCACAAATGTAGTACTTGGGGATGACAAGACAGTATTGGAGATTCATGTTGAATATGACCGTGAAAAGCGCACCAAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT