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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttataatacctgcaacgttttatagttgccctttctggcgtaatatgacattgtacaatgttctcctttaccattgtatggtgtgatgttcacctgctataattaacatcctaattttattttttgacttgatcgattacag

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 5'ss of exon 12
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 18
GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttataatacctgcaacgttttatagttgccctttctggcgtaatatgacattgtacaatgttctcctttaccattgtatggtgtgatgttcacctgctataattaacatcctaattttattttttgacttgatcgattacag
||||| ||||| ||||||||||| |||||||||||||| || || ||  |  |||  || ||    |||     ||  |||    || ||| |  |       |||   |  |||   |  || |   |||    ||| ||   |||    ||  ||  ||   |  |  | ||  || ||  |  | | |||    | || |  |  ||  |        
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCGgtatgtt----tatctgtattg-------gttaaacaatctaatgccatgtctaatt---taatcttgaactt----atgatagagtagcaaatctaact-ttagaacgagta-cttaagaaaacttctctaactgcgcag------
















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|162176172|gb|FC351914.1|FC351914
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|15320332|gb|BI488151.1|BI488151
EST:     TGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: TGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|162165708|gb|FC340889.1|FC340889
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|208386538|gb|DC952747.1|DC952747
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|67697462|gb|BJ957695.1|BJ957695
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|37823157|gb|BJ581223.1|BJ581223
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|208388659|gb|DC953435.1|DC953435
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|37847922|gb|BJ605930.1|BJ605930
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|37835509|gb|BJ593521.1|BJ593521
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|162152561|gb|FC328839.1|FC328839
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|67724660|gb|BJ974919.1|BJ974919
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|162194037|gb|FC370212.1|FC370212
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|208356950|gb|DC922286.1|DC922286
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTTTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|162234310|gb|FC409848.1|FC409848
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|37825198|gb|BJ583264.1|BJ583264
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
EST: gi|162202112|gb|FC378033.1|FC378033
EST:     GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA                         CTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA
genomic: GATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttata ... tcgattacagCTACTACACTGTGCTTTTTGGAGTATCACGTGCCATGGGTGTCCTCTCTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAAgtgagttataatacctgcaacgttttatagttgccctttctggcgtaatatgacattgtacaatgttctcctttaccattgtatggtgtgatgttcacctgctataattaacatcctaattttattttttgacttgatcgattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC