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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcagattttgggtactacatcgggggtgtctcgaggaatgatgtgattccatggtgatcttctttgcggtacttaattttttttaagtgtccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGAGGATCCGCCGGCGAGAGCAGACGATGAGGGCGATGGTGCGTCAAAGGGT

Basic information

species Physcomitrella patens
transcript PP1S99_240V6.1
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|100424439|gb|BY958485.1|BY958485
EST:     CGTGGGAGTTTGAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: CGTGGGAGTTTGAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
EST: gi|18326787|gb|BJ158787.1|BJ158787
EST:     CGTGGGAGTTTGAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: CGTGGGAGTTTGAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
EST: gi|18364027|gb|BJ196100.1|BJ196100
EST:     GGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: GGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
EST: gi|18365849|gb|BJ197927.1|BJ197927
EST:     GAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: GAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
EST: gi|18364469|gb|BJ196542.1|BJ196542
EST:     GAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: GAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
EST: gi|18359123|gb|BJ191183.1|BJ191183
EST:     GGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: GGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
EST: gi|100427823|gb|BY959142.1|BY959142
EST:     CGTGGGAGTTTGAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAG                         GTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA
genomic: CGTGGGAGTTTGAGGTCGGCTTTTGGCGAATTGAATGCAGCGGCAGTGAGgtactgccgt ... ccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attccatggtgatcttctttgcggtacttaattttttttaagtgtccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGAGGATCCGCCGGCGAGAGCAGACGATGAGGGCGATGGTGCGTCAAAGGGT
                         acttaat  putative branch site (score: 4)
                        tacttaatttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagattttgggtactacatcgggggtgtctcgaggaatgatgtgattccatggtgatcttctttgcggtacttaattttttttaagtgtccatatgcagGTTTTCTCTGGAAATGATTTCGGAGGGAAAACCTGCTGCTGTGATTGCGGAGGATCCGCCGGCGAGAGCAGACGATGAGGGCGATGGTGCGTCAAAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG