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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatacaattgtgctttcgcctaaaaaaaactttacacatccttgaaatggccaggggcaagcgttgaggttaagctctaacctctgtttggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATGATTACTCGAAAG

Basic information

species Physcomitrella patens
transcript PP1S279_72V6.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S279_72V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G17450.1 (Glycine max), 3'ss of exon 6
catatacaattgtgct--ttcgcctaaaaaaaactttacacatccttgaaatggccaggggcaagcgttgaggttaagctctaacctctgtttggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATGATTACTCGAAAG
   |||  ||| | ||  ||    ||   ||    ||   |||   | | |   | |      | |     || |    | || ||||| |  | || |||| | || |||||||||||||| || ||||| ||||| ||||| |||||||||||||||||||||
-gaatatgattttactgattttaatattcaatttcttcttcataaatcataatcctaatatttatctacatggctcgtattta-cctctttgggatttgcagCCTGTAGGGGTTGTAGGTGCAATTACACCTTGGAACTTTCCCCTTGCTATGATTACTCGAAAG

upper sequence: PP1S279_72V6.3 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G41690.1 (Glycine max), 3'ss of exon 6
catatacaattgtgctttcgcctaaaaaaaactttacacatccttgaaatggccaggggcaagcgttgaggttaagctctaacctctgtttggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATGATTACTCGAAAG
  |     | | || |||  |  |    ||  || |        |  |    ||           |  | |    |   | | |||| |  | || |||| | || |||||||||||||| || ||||| ||||| ||||| |||||||||||||||||||||
agttctagaatatgattttactgattttaatattcaatttcttcttcataatcctaatatttatatacatggctcgtatttatctctttgggatttgcagCCTGTAGGGGTTGTAGGTGCAATTACACCTTGGAACTTTCCCCTTGCTATGATTACTCGAAAG
















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|162170327|gb|FC346524.1|FC346524
EST:     ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAG                         GCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
genomic: ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAGgtgagaccgt ... tggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
EST: gi|208391821|gb|DC937997.1|DC937997
EST:     ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAG                         GCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
genomic: ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAGgtgagaccgt ... tggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
EST: gi|19789205|gb|BQ041166.1|BQ041166
EST:     ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAG                         GCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
genomic: ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAGgtgagaccgt ... tggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
EST: gi|100371823|gb|BY967570.1|BY967570
EST:     ATATTATACCCTCTCCTTTTCCAACTNAACGTATGCTAGTAATGAAACAG                         GCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG
genomic: ATATTATACCCTCTCCTTTTCCAACTAAACGTATGCTAGTAATGAAACAGgtgagaccgt ... tggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatggccaggggcaagcgttgaggttaagctctaacctctgtttggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATGATTACTCGAAAG
                               ctctaac  putative branch site (score: 2)
                                     cctctgttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatacaattgtgctttcgcctaaaaaaaactttacacatccttgaaatggccaggggcaagcgttgaggttaagctctaacctctgtttggttggcagGCAGTTGGGGTTGTAGGTGCTATCACACCATGGAATTTTCCGCTTGCTATGATTACTCGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA