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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaactcgtgcttacattttttttggtcgtgttttgtaatcatgttcgtggtggcaaatgtaacttctaaattcgttttaacctggtctggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAAAACGAACCCGTATGGATATCGAGGCCAACAAGAACTGGAGGTCACCACA

Basic information

species Physcomitrella patens
transcript PP1S101_67V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S101_67V6.2 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------------aagaactcgtgcttacattttttttggtcgtgttttgtaatcatgttcgtggtggcaaatgtaacttctaaattcgttttaac-ctggtctggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAAAACGAACCCGTATGGATATCGAGGCCAACAAGAACTGGAGGTCA-CCACA-
                                                                                                 | || ||| |||   ||||  |  |         | ||   | |  |  | ||| |   || |   ||| | | ||   |  |||  |||  ||| || || | ||||||  | |||||||| |||||||||||||||||||| |  |  ||||| ||||| ||| |||  ||    |  |    | | | ||||  
gtaagtgttaattggctcctcctcctgaatatcctagatagataataaaagcttaatagtatgaaacaagtttttcttgataaattctggttttgtgtagtactttcatgcattttacttttaaaaaacttttattcacttcttttccaattttgttttttttttcttctaaaaattcatcttacgtggcagGGCAAAATATGGCATTGATGAGATGTGCCGTGATCAATGGAATTGGGCTAGCAAAAACCCTTATGGCTATGGAGATCAG--GGCTCCACCGATTAACCACTT
















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|37821921|gb|BJ579987.1|BJ579987
EST:     AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTT-G-G                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
EST: gi|208351996|gb|DC925805.1|DC925805
EST:     AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAG                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
EST: gi|208388227|gb|DC956977.1|DC956977
EST:     AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAG                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
EST: gi|37830550|gb|BJ588562.1|BJ588562
EST:     AAAGCAGAAAAGGAGTTAGGTTGGAG                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
EST: gi|208382034|gb|DC919921.1|DC919921
EST:     AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAG                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
EST: gi|208363974|gb|DC947218.1|DC947218
EST:     AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAG                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
EST: gi|208358116|gb|DC946744.1|DC946744
EST:     AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAG                         AGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA
genomic: AGTGAGGTCTTTGCTTCAACTGAGAAAGCAGAAAAGGAGTTAGGTTGGAGgtgatttatt ... ggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtggtggcaaatgtaacttctaaattcgttttaacctggtctggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAAAACGAACCCGTATGGATATCGAGGCCAACAAGAACTGGAGGTCACCACA
                               ttttaac  putative branch site (score: 2)
                       taaattcgttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaactcgtgcttacattttttttggtcgtgttttgtaatcatgttcgtggtggcaaatgtaacttctaaattcgttttaacctggtctggcgttacagAGCCAAGTTTGGCATAAAAGAGATGTGTCGTGATCAATGGAATTGGGCAAAAACGAACCCGTATGGATATCGAGGCCAACAAGAACTGGAGGTCACCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG