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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcacagcttctgagattgtcctgcaatatattctttgatcttggtcaaactctaaccgaggcccattttccttgtcataattctgaatacggacagttttcccatttggcatttagctgtaatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGTATTGACATTGCCGAAGGCTCG

Basic information

species Physcomitrella patens
transcript PP1S49_100V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_100V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 3
gtgcacagcttctgagattgtcctgcaatatattctttgatcttggtcaaactctaaccgaggcccattttccttgtcataattctgaatac--ggacagttttcccatttggcatttagctgtaatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGTATTGACATTGCCGAAGGCTCG
                                        | ||  |     |  |   |  |   || | ||     | | |      | |  ||  |    |||  ||| |  |||     |  | |  ||||| || ||||| ||||| |||||||||||   |||||| || || ||||||||||||||||| |||||||||
---------------------------------------gtgttaat-ggttttcatttgttgtttatataccaaaagacattctcagtttcttggctaaccatccttttttg--tttcataatgtttac-cagGGTGGTGATCTTATCAAATGGGACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCG

upper sequence: PP1S49_100V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 3
gtgcacagcttctgagattgtcctgcaatatattctttgatcttggtcaaactctaaccgaggcccattttccttgtcataattctgaatacggacagttttcccatttggcatttagctgtaatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGTATTGACATTGCCGAAGGCTCG
                              | ||| | | | |  ||         ||| |    ||||  |  | || |   |            | |  |||  |||    |||     |  | |  ||||| || ||||| ||||| |||||||||||   |||||| || || ||||||||||||||||| |||||||| 
-----------------------------gtcttcatggttttcagttgtttatataccaaaagtcattcccagtttcttggct------------aatcatccttttt----tttcataatgtttac-cagGGTGGTGATCTTATCAAATGGGACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCA

upper sequence: PP1S49_100V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 4
gtgcacagcttctgagattgtcctgcaatatattctttgatcttggtcaaactctaaccgaggcccattttccttgtcataattctgaatacggacagttttcccatttggcatttagctgtaatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGTATTGACATTGCCGAAGGCTCG----
                       ||  |    || |  | | ||| | | |  | ||  ||    |||| ||  | || |    || |  |  ||     | |   ||||   |||     |  | |  ||||| || ||||| ||||| |||||| ||||   |||||| || || ||||||||||||||||| |||||||||    
----------------------gtgttaatggttttcagttgttgtttatataccaaaaga----cattctcagtttcttgg--ctaaccatagagtccatccttttttg---tttcataatgtttac-cagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT

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|162185816|gb|FC362372.1|FC362372
EST:     AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAG                         GGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGT
genomic: AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAGgtgcacagct ... aatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGT
EST: gi|18351314|gb|BJ183366.1|BJ183366
EST:     AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAG                         GGGGGAGATCTGATCAAGTGGG
genomic: AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAGgtgcacagct ... aatgatgcagGGGGGAGATCTGATCAAGTGGG
EST: gi|18351940|gb|BJ183992.1|BJ183992
EST:     AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAG                         GGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGT
genomic: AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAGgtgcacagct ... aatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGT
EST: gi|100414488|gb|BY992798.1|BY992798
EST:     AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAG                         GGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGT
genomic: AAATCTACACGCAACGGGGAGATACAGTTCTTGATATGGCTTGTGGAAAGgtgcacagct ... aatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataattctgaatacggacagttttcccatttggcatttagctgtaatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGTATTGACATTGCCGAAGGCTCG
                                            taatgat  TA-rich tract