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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatctattccgttttctgtttattcaactctctgatcacctgtgcatttctagaatgtggaattcgttcggggttacttgattttcagattttgagtgcctgtacgagcgcagGAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTGCAGCAAAGAGCGGTGATTGCGGAGAAAGCATTACGAGAGAAAGAGGAAG

Basic information

species Physcomitrella patens
transcript PP1S199_21V6.1
intron # 22
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|162182859|gb|FC358943.1|FC358943
EST:     GTATCAAGGAAATTTACGAAATGGCTACGACGAAACGTTTTGAATCTGAG                         GAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTG
genomic: GTATCAAGGAAATTTACGAAATGGCTACGACGAAACGTTTTGAATCTGAGgtacatctat ... acgagcgcagGAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTG
EST: gi|162170523|gb|FC347669.1|FC347669
EST:     GTATCAAGGAAATTTACGAAATGGCTACGACGAAACGTTTTGAATCTGAG                         GAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTG
genomic: GTATCAAGGAAATTTACGAAATGGCTACGACGAAACGTTTTGAATCTGAGgtacatctat ... acgagcgcagGAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaattcgttcggggttacttgattttcagattttgagtgcctgtacgagcgcagGAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTGCAGCAAAGAGCGGTGATTGCGGAGAAAGCATTACGAGAGAAAGAGGAAG
                 acttgat  putative branch site (score: 5)
                   ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatctattccgttttctgtttattcaactctctgatcacctgtgcatttctagaatgtggaattcgttcggggttacttgattttcagattttgagtgcctgtacgagcgcagGAACAGAACGAAGCAACCATTAGGGTAAGGCCTTCGTACGTTTTAGAGCTGCAGCAAAGAGCGGTGATTGCGGAGAAAGCATTACGAGAGAAAGAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA