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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactagcatgagatatctgatatgttaaagcattttacagcggtgaagaaattaacgactttgtctatcacatcaaaagttaacatggctttcgtagaacgtatacatgctcagagtggttaaacttaatttgtggtgttttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACGACTTTCATTGAACAGAAACTGG

Basic information

species Physcomitrella patens
transcript PP1S152_87V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 10
gtaaaactagcatgagatatctgatatgttaaagcattttacagcggtgaagaaattaacgactttgtctatcacatcaaaagttaacatggctt-tcgtagaacgtatacatgctcagagtggttaaacttaatttgtggtgttttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACGACTTTCATTGAACAGAAACTGG
                                                   ||   | |    || | ||||| ||     ||||  |    ||  |  |     |||||| | |||  | |  ||   ||    ||||    ||  |||    |||||||||||| ||||||||||||||||||||||| || ||||| ||||| || || |||||  ||||||| |
-------------------------------------------------gtgaggctcattttttgggctatctcagacctagttttctaacctcatacttctctgtatactttctcttaattcttttcctcctcttgtt---ttccata----gCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG

upper sequence: PP1S152_87V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 10
gtaaaactagcatgagatatctgatatgttaaagcattttacagcggtgaagaaattaacgactttgtctatcacat-caaaagttaacatggctttcgtagaacgtatacatgctcagagtggttaaacttaatttgtggtgttttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACGACTTTCATTGAACAGAAACTGG
                                                   ||   | |    |||  ||||| ||  |  |  ||||| |     |  |     |||||| | |||  | |  ||   ||    ||||    ||  |||    |||||||||||| ||||||||||||||||||||||| || ||||| ||||| || || |||||  ||||||| |
-------------------------------------------------gtgaggctcatttttttagctatctcagacctagtttaacctcatacttctc---tgtatacttcctcttaattcttttcctcctcttgtt---ttccata----gCATCCTGGAACAACTATTGTCACAGACAGTGTGACTTCTGATGGGCTTACCACGTTTATTGAGAAGAAACTTG
















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|162196621|gb|FC374911.1|FC374911
EST:     CTGCAATTGTGTTGGAGCAG                         CATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
genomic: CTGCAATTGTGTTGGAGCAGgtaaaactag ... ttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
EST: gi|37850442|gb|BJ608450.1|BJ608450
EST:     TTCTGGCTGCAATTGTGTTGGAGCAG                         CATCCTGGAACCACTATTGTCACAGACAGTGTGACNTCGGATGGCCTTACG
genomic: TTCTGGCTGCAATTGTGTTGGAGCAGgtaaaactag ... ttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
EST: gi|162192137|gb|FC368286.1|FC368286
EST:     TGGCTGCAATTGTGTTGGAGCAG                         CATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
genomic: TGGCTGCAATTGTGTTGGAGCAGgtaaaactag ... ttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
EST: gi|162192138|gb|FC368287.1|FC368287
EST:     GCAACCGCCTTATTGCTCTTCTGGCTGCAATTGTGTTGGAGCAG                         CATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
genomic: GCAACCGCCTTATTGCTCTTCTGGCTGCAATTGTGTTGGAGCAGgtaaaactag ... ttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
EST: gi|162196876|gb|FC375153.1|FC375153
EST:     TGAATCGCAACCGCCTTATTGCTCTTCTGGCTGCAATTGTGTTGGAGCAG                         CATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
genomic: TGAATCGCAACCGCCTTATTGCTCTTCTGGCTGCAATTGTGTTGGAGCAGgtaaaactag ... ttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
EST: gi|162215700|gb|FC391415.1|FC391415
EST:     TGAATCGCAACCGCCTTATTGCTCTTCTGGCTGCAATTGTGTTGGAGCAG                         CATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG
genomic: TGAATCGCAACCGCCTTATTGCTCTTCTGGCTGCAATTGTGTTGGAGCAGgtaaaactag ... ttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaacgtatacatgctcagagtggttaaacttaatttgtggtgttttataatcagCATCCTGGAACCACTATTGTCACAGACAGTGTGACCTCGGATGGCCTTACGACTTTCATTGAACAGAAACTGG
                            acttaat  putative branch site (score: 4)
                        ttaaacttaatttgt  TA-rich tract