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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcacatttttttatcgtgcttttctgtatttaagaatgccaaagttgacatttcgtaaactgtctttaatgtcgtagacttactctcgtgggttcattggtgattgatataattttcttttttttcgtatcctccatgttatttgcttcattgttttgtactttttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG

Basic information

species Physcomitrella patens
transcript PP1S60_221V6.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA05G08040.1 (Glycine max), 3'ss of exon 17
gtctgcacatttttttatcgtgcttttctgtatttaagaatgccaaagttgacatttcgtaaactgtctttaatgtcgtagacttactctcgtgggttcattggtgattgatataattttcttttttttcgtatcc-tccatgttatttgcttcattgttttgtactttttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG
                                                                      | ||||    ||  ||   |      |   | | |  |||||| |||| | | |    |  |||   | |   | | | | ||||   |||||| |   |      |||||||||||  | |||||  | ||||| ||||||||||| |||||||||||||||||||||||  ||||||| |||||  | ||||| || ||| || || 
---------------------------------------------------------------------ctgatgtatgtgatatataat-----ataattcgttttttgataaaattatgtataaaataatatatattctcataaatggattcaaacttttgtgcggatg-----cagGTTGGTGGCATCTATGTTAGGTTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCAT

upper sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 18
gtctgcacatttttttatcgtgcttttctgtatttaagaatgccaaagttgacatttcgtaaactgtctttaatgtcgtagacttactctcgtgggttcattggtgattgatataattttcttttt-----tttcgtatc---ctccatgttatttgcttcattgttttgtactttt---tatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG
                                                                                             |  ||||   |  ||  || | ||||| ||||      ||  ||||        || || | |  |  || | |||  ||||||   |     |||||||||||  | |||||  |  |||| ||||||||||| |||||||||||||||||||||||  ||||||| |||||  | ||||| || ||| || |  
---------------------------------------------------------------------------------------------gtattcaccagatat--atgtgatttttttttataaaattatgtatagaataatatattttctcataaatggatttcaacttttgtgtggatgcagGTTGGTGGCATCTATGTTAGGCTGTTTCTGAAAGATCCCAAATTCCCTCTTAGAAACCCTAAAAGGTTCTTGGAAGGTCTACTAGATCAGTATTTGTCGT

upper sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: Vv11s0016g04420.t01 (Vitis vinifera), 3'ss of exon 17
gtctgcacatttttttatcgtgcttttctgtatttaagaatgccaaagttgacatttcgtaaactgtctttaatgtcgtagacttactctcgtgggttcattggtgattgatataattttcttttttttcgtat-cctccatgttatttgcttcattgttttgtactttttatcct-cagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG
                                                                                                 |   |  || |  ||    |  | ||| ||    |||    |  |  | ||   |  ||| |    |  |  |  || | |||||||| ||| | |||||  |  | ||| |||||||||| || || ||||||||||| || ||| ||||||| |||||  |||||||||| ||| |  || 
------------------------------------------------------------------------------------------------gtatctcctgttctattctgtcctttttattcaaatatgtacctgtactgttgagtggatt-tcaaattttcatggtcatgcagGTTGGAGGAATCTATGTTAGGCTTTTCTTGAAAGATCCCAAGTTTCCTCTTAGAAATCCAAAGAGGTTCTTGGAAGGACTGCTAGACCAGTATCTTTCAT

upper sequence: PP1S60_221V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: EFJ24089 (Selaginella moellendorffii), 3'ss of exon 18
gtctgcacatttttttatcgtgcttttctgtatttaagaatgccaaagttgacatttcgtaaactgtctttaatgtcgtagacttactctcgtgggttcattggtgattgatataattttcttttttttcgtatcctccatgttatttgcttcattgttttgtactttttatcct-cagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG
                                                                                                                 ||  ||| |||  || |  |  ||       || |     |  | ||| || || ||    | |||||||| |||||||| ||  | |||||||||||||||||||| || |||||| | || || ||| |||| || |||||  | || || || |||||  | |
----------------------------------------------------------------------------------------------------------------gtagatttttttaattcctcaatctttg----atctatcgtaacgcttt-tatttcttgctgtgcagGTTGGCGGAGTGTACGTAAGATTGTTCCTGAAAGATCCAAAGTTTCCTCTTCGGAATCCCAAGAGGTTTTTGGAAGGACTTCTGGATCAGTATGTAGCCG

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|162151271|gb|FC327725.1|FC327725
EST:     ATCTTCCTGAGAATTCATCTGGGCAGCAAGTCGTCAATGATGAACCTCAG                         GTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTT
genomic: ATCTTCCTGAGAATTCATCTGGGCAGCAAGTCGTCAATGATGAACCTCAGgtctgcacat ... ttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTT
EST: gi|162193747|gb|FC371274.1|FC371274
EST:     ATCTTCCTGAGAATTCATCTGGGCAGCAAGTCGTCAATGATGAACCTCAG                         GTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTT
genomic: ATCTTCCTGAGAATTCATCTGGGCAGCAAGTCGTCAATGATGAACCTCAGgtctgcacat ... ttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTT
EST: gi|100420945|gb|BY993538.1|BY993538
EST:     ATCTTCCTGAGAATTCATCTGGGCAGCAAGTCGTCAATGATGAACCTCAG                         GTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTT
genomic: ATCTTCCTGAGAATTCATCTGGGCAGCAAGTCGTCAATGATGAACCTCAGgtctgcacat ... ttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcgtatcctccatgttatttgcttcattgttttgtactttttatcctcagGTTGGTGGAGTGTATGTCCGCTTGTTCCTGAAAGATCCAAAATTCCCTCTTAGAAACCCTAAGCGGTTCTTAGAAGGGTTGCTAGACCAATATGTGACAG
                                       tactttttatcctc  CT-rich tract
                                  ttttgtactttttat  TA-rich tract