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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgcattcgtttagtgcagcctctggatatgttttagtgaattgcattattgtgtttgagatactattctcgcttttaatttatgttttcaacattcttgtttgagttaagcatcgtctattctggttatgaatcgcaaacatgctgttcgctatgaataacgccccataattcgtactttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG

Basic information

species Physcomitrella patens
transcript PP1S397_39V6.2
intron # 3
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|37835032|gb|BJ593044.1|BJ593044
EST:     GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG                         GGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
genomic: GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAGgtaagtcgca ... tttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
EST: gi|7583218|gb|AW699382.1|AW699382
EST:     GTTGAAACTTGGCTGAATTTGACGGTACCAGAG                         GGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
genomic: GTTGAAACTTGGCTGAATTTGACGGTACCAGAGgtaagtcgca ... tttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
EST: gi|15327404|gb|BI488043.1|BI488043
EST:     TTGAAACTTGGCTGAATTTGACGGTACCAGAG                         GGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
genomic: TTGAAACTTGGCTGAATTTGACGGTACCAGAGgtaagtcgca ... tttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
EST: gi|162267552|gb|FC444303.1|FC444303
EST:     GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG                         GGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
genomic: GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAGgtaagtcgca ... tttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
EST: gi|162267551|gb|FC444302.1|FC444302
EST:     GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG                         GGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
genomic: GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAGgtaagtcgca ... tttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
EST: gi|18336855|gb|BJ168878.1|BJ168878
EST:     GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAG                         GGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
genomic: GCGATGTCCGCGATGATGTTGAAACTTGGCTGAATTTGACGGTACCAGAGgtaagtcgca ... tttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcaaacatgctgttcgctatgaataacgccccataattcgtactttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG
                      gaataac  putative branch site (score: 2)
                                            ctttact  putative PPT
                   tatgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgcattcgtttagtgcagcctctggatatgttttagtgaattgcattattgtgtttgagatactattctcgcttttaatttatgttttcaacattcttgtttgagttaagcatcgtctattctggttatgaatcgcaaacatgctgttcgctatgaataacgccccataattcgtactttactgtagGGAAGAAAAGCTCCTTGGAAACACACGATGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG