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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATCTTTCAGGAAGCTGGCCTTCCTCTTTGGCTACGCCCGTATGAGGTCATTGTTACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACGgtgagctttttattggacctcatggtaatgaacataactggtgatgtgagatttgattggtcagaccgacttaccgtcagccagttacattctgtatgtg...

Basic information

species Physcomitrella patens
transcript PP1S113_110V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S113_110V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ26597 (Selaginella moellendorffii), 5'ss of exon 9
ACATCTTTCAGGAAGCTGGCCTTCCTCTTTGGCTACGCCCGTATGAGGTCATTGTTACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACGgtgagctttttattggacctcatggtaatgaacataactggtgatgtgagatttgattggtcagaccgacttaccgtcagccagttacattctgtatgtg
|||| ||||||||||||||||||||||| ||| | || || ||||||||  | || || || ||     |||| ||||||||||| |||   || || ||  | | |||      | |  ||||  |        ||  | || ||     | |  |                                         
ACATTTTTCAGGAAGCTGGCCTTCCTCTATGGTTGCGTCCATATGAGGTTCTAGTGACTTCCTCCAGAGCAGCGCTGATTGAGACGATTCCGGACACTgtaggttctttt-----cgttttggt--ttgtttcctctactaatatgctgcgttacag-----------------------------------------

upper sequence: PP1S113_110V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ06373 (Selaginella moellendorffii), 5'ss of exon 11
ACATCTTTCAGGAAGCTGGCCTTCCTCTTTGGCTACGCCCGTATGAGGTCATTGTTACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACGgtgagctttttattggacctcatggtaatgaacataactggtgatgtgagatttgattggtcagaccgacttaccgtcagccagttacattctgtatgtg
|||| ||||||||||||||||||||||| ||| | || || ||||||||  | || || || ||     |||| ||||||||||| |||   || || ||  | | ||| |||    |  ||||           ||  | || ||     | |  |                                         
ACATTTTTCAGGAAGCTGGCCTTCCTCTATGGTTGCGTCCATATGAGGTTCTAGTGACTTCCTCCAGAGCAGCGCTGATTGAGACGATTCCGGACACTgtaggttcttt-ttg----ttttggt--ctgtttcctctactaatatgctgcgttacag-----------------------------------------
















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|162177674|gb|FC353260.1|FC353260
EST:     TCATTGTTACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACG                         GCTTCAATTCATTCCATCAAAAGTAGGAATAATGATGTGACCAGCTTACGG
genomic: TCATTGTTACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACGgtgagctttt ... tgttcctcagGCTTCAATTCATTCCATCAAAAGTAGGAATAGTGATGTGACCAGCTTACGG
EST: gi|161982255|gb|EE296241.1|EE296241
EST:     CATTGTTAACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACG                         GCTTCAATTCATTCCATCAAAAGTAGGAATAGTGATGTGACCAGCTTACGG
genomic: CATTGTT-ACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACGgtgagctttt ... tgttcctcagGCTTCAATTCATTCCATCAAAAGTAGGAATAGTGATGTGACCAGCTTACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATCTTTCAGGAAGCTGGCCTTCCTCTTTGGCTACGCCCGTATGAGGTCATTGTTACATCTTCACATACAGCTCTGATTGAGACCATTTACGATACGgtgagctttttattggacctcatggtaatgaacataactggtgatgtgagatttgattggtcagaccgacttaccgtcagccagttacattctgtatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC