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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatccttttccctgtcgatttataatgagtcgcaatctttcgcgctaatgcaacttaatctttctaatccaatggacttacaagtcgtgaaaccgtgtggtattttattgatatgctaaaagtgatttgaatggatgaatcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATGGTGTGGTTCGTTTCGCCCAAGAAAACAGCGGGCTGCAAGAATGCAGCAT

Basic information

species Physcomitrella patens
transcript PP1S98_113V6.5
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|37847051|gb|BJ605059.1|BJ605059
EST:     GAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: GAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37847630|gb|BJ605638.1|BJ605638
EST:     TTCCGAGTCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: TTCCGAGTCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37828279|gb|BJ586291.1|BJ586291
EST:     AAGTATTCCGAGTCCATGTTTGCCAAAACCCANCCGGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: AAGTATTCCGAGTCCATGTTTGCCAAAACCCAACC-GAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37836088|gb|BJ594096.1|BJ594096
EST:     CCGAGTCCATGTTTGCCAAAAACCAACNGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: CCGAGTCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37839578|gb|BJ597586.1|BJ597586
EST:     CAAGTATTCCGAGTCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: CAAGTATTCCGAGTCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37834923|gb|BJ592935.1|BJ592935
EST:     AAGTATTCCGAGTCCATGTTTGCCAAAACCCAACCGGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: AAGTATTCCGAGTCCATGTTTGCCAAAACCCAACC-GAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37836995|gb|BJ595003.1|BJ595003
EST:     CAAGTATTCCGAGTCCATGTTTGCCAAAACCCANCNGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: CAAGTATTCCGAGTCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
EST: gi|37847120|gb|BJ605128.1|BJ605128
EST:     AAGTATTCCGAGTCCCATGTTTGCCAAAACCCAACCGAATTCATCCGCTT                         GCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG
genomic: AAGTATTCCGAGT-CCATGTTTGCCAAAACCCAACCGAATTCATCCGCTTgtgagatcct ... tcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtggtattttattgatatgctaaaagtgatttgaatggatgaatcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATGGTGTGGTTCGTTTCGCCCAAGAAAACAGCGGGCTGCAAGAATGCAGCAT
                   tgctaaa  putative branch site (score: 2)
      tattttattgatatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatccttttccctgtcgatttataatgagtcgcaatctttcgcgctaatgcaacttaatctttctaatccaatggacttacaagtcgtgaaaccgtgtggtattttattgatatgctaaaagtgatttgaatggatgaatcgacctcagGCGTGCCGATGACGATTGCTGTGGCGGAATTCAAGGGTCCAGACGTGCATGGTGTGGTTCGTTTCGCCCAAGAAAACAGCGGGCTGCAAGAATGCAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA