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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcaagcatttcaaatgtgtcatcagactgcattattcttctgccgctctttggtatccgaacgtccttattttcagagaacgaggttgtgtaacaatcagatgggtagtgtgtgattcaagttttgatcgcgagttaaatcgtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGACTGCGTTATCGAGCGCTGCAGTTTTGCAAACATGAGACGAGTGCTCCTCG

Basic information

species Physcomitrella patens
transcript PP1S94_62V6.1
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|67702268|gb|BJ962501.1|BJ962501
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
EST: gi|100371537|gb|BY968028.1|BY968028
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
EST: gi|18362301|gb|BJ194371.1|BJ194371
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
EST: gi|18362116|gb|BJ194184.1|BJ194184
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
EST: gi|18374815|gb|BJ206393.1|BJ206393
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
EST: gi|18375274|gb|BJ206852.1|BJ206852
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
EST: gi|18373654|gb|BJ205232.1|BJ205232
EST:     TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAG                         TTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC
genomic: TCGCAGTCGAGGAGTGTATGCAGTTAAAATGCACTCAGCAGCTTCGATAGgtgtgcaagc ... gtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatgggtagtgtgtgattcaagttttgatcgcgagttaaatcgtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGACTGCGTTATCGAGCGCTGCAGTTTTGCAAACATGAGACGAGTGCTCCTCG
                         ttttgat  putative branch site (score: 4)
                                           tcgttttt  putative PPT
                                    agttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgcaagcatttcaaatgtgtcatcagactgcattattcttctgccgctctttggtatccgaacgtccttattttcagagaacgaggttgtgtaacaatcagatgggtagtgtgtgattcaagttttgatcgcgagttaaatcgtttttgcagTTTTCAAGGTACAACAGAATTGCAATGCTAAATCTCGATGAGATGAGAGACTGCGTTATCGAGCGCTGCAGTTTTGCAAACATGAGACGAGTGCTCCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC