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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtctcacaaacccgtgtcttgtttgttctcgtttgttgctcttcttggttcgcaactataatctttgttaccttcgcatttcgcttgagatttattgaagattaaagcaatgaagtaaaccttgtttttctttcttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGGGGAAGCAAGAGCAAGATGACTTTTATACAGCAGAGGAAAACATCCACCG

Basic information

species Physcomitrella patens
transcript PP1S9_212V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_212V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os04g02500.2 (Oryza sativa), 3'ss of exon 2
gtgtgtctcacaaacccgtgtcttgtttgttctcgtttgttgctcttcttggttcgcaactataatctttgttaccttcgcatttcgcttgagatttattgaagattaaagcaatgaagtaaaccttgtttttctttcttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGGGGAAGCAAGAGCAAGATGACTTTTATACAGCAGAGGAAAACATCCACCG
                                          || |  ||| ||   ||  | ||   |  |  | ||   ||||      | | || | | |  || |  | |  | |    || | || |  ||  |  | | |||||||    || ||||| ||||||||| |  |||| |||||  | || |||||||||||||||||||||||||| |  ||| |||| || ||  | ||  |
-----------------------------------------actatcattgattaaaaaaaa-aacagtcatcgctttaatattttctgctaaaattctggcaccttca--cgacaatg----cccttttctctttaatgttatatagGTATAACAGAGCCAATAAAAGCTGGTATCAGAGATGCAAAATTGGGTGTGGGGAAGCAAGAGCAAGATGACTTCTTCACATCAGAAGATAATGTGCAAAG
















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|18360457|gb|BJ192519.1|BJ192519
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|18365765|gb|BJ197842.1|BJ197842
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|37847696|gb|BJ605704.1|BJ605704
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|37838432|gb|BJ596440.1|BJ596440
EST:     CNTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|18367233|gb|BJ199314.1|BJ199314
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTT
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTT
EST: gi|67697114|gb|BJ957347.1|BJ957347
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|67573726|gb|BJ946550.1|BJ946550
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|37846217|gb|BJ604225.1|BJ604225
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|18330997|gb|BJ163003.1|BJ163003
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG
EST: gi|100389063|gb|BY952267.1|BY952267
EST:     CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAG                         GTATTGTTGAACCAACCAAAGCTGGTGTTCGAGACGCANAGCTTGGAGTGG
genomic: CCTCCAGAAGATGGGGTGGAGAGGGAAAGGGCTTGGTAAAAACGAACAAGgtgtgtctca ... ttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattgaagattaaagcaatgaagtaaaccttgtttttctttcttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGGGGAAGCAAGAGCAAGATGACTTTTATACAGCAGAGGAAAACATCCACCG
                              ccttgtttttctttct  CT-rich tract
        aagattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtctcacaaacccgtgtcttgtttgttctcgtttgttgctcttcttggttcgcaactataatctttgttaccttcgcatttcgcttgagatttattgaagattaaagcaatgaagtaaaccttgtttttctttcttgtgtgtagGTATTGTTGAACCAATCAAAGCTGGTGTTCGAGACGCAAAGCTTGGAGTGGGGAAGCAAGAGCAAGATGACTTTTATACAGCAGAGGAAAACATCCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA