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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcactgtgcctggagtttgatcaattggactggggaatggggacgtgtgtgcatgcgattatggtgattgggcttgtggttgattgatgtcggttaggatgatcggcgctgatgctgttcgtgtgagtgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATGATTTGAAGGCGTTGCAGAGCGTGGGTCAAATCATCGGAGAAGTGTTGAG

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.2
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|18356521|gb|BJ188580.1|BJ188580
EST:     AAGAGCTCGATGCAAGGCTGCNAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: AAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|18353546|gb|BJ185601.1|BJ185601
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|18330767|gb|BJ162773.1|BJ162773
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|100450689|gb|CJ974389.1|CJ974389
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|18358089|gb|BJ190148.1|BJ190148
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGC
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGC
EST: gi|18353444|gb|BJ185499.1|BJ185499
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|208398538|gb|DC912383.1|DC912383
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|18357042|gb|BJ189101.1|BJ189101
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|100405000|gb|BY991388.1|BY991388
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|162269527|gb|FC445083.1|FC445083
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
EST: gi|18344191|gb|BJ176230.1|BJ176230
EST:     TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATT                         TGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG
genomic: TAGGCGCAAGCTTTTGCAGCACAAAGAGCTCGATGCAAGGCTGCGAAATTgtgagcactg ... tgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatgtcggttaggatgatcggcgctgatgctgttcgtgtgagtgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATGATTTGAAGGCGTTGCAGAGCGTGGGTCAAATCATCGGAGAAGTGTTGAG
                        cgctgat  putative branch site (score: 4)
                                                 tatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcactgtgcctggagtttgatcaattggactggggaatggggacgtgtgtgcatgcgattatggtgattgggcttgtggttgattgatgtcggttaggatgatcggcgctgatgctgttcgtgtgagtgggtattagTGCGTGAAAATGTGAAGGCTGCGAGGAAAGAGTTTGACAAGACAGAAGATGATTTGAAGGCGTTGCAGAGCGTGGGTCAAATCATCGGAGAAGTGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT