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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacattcgtgttcttttaagtaggcgcgaatcacctaaaaattttagaattaggattaggttaattttctagctaatcatcataataatttcgtgcgcagaagggaacctggaggctggccagactctaattcagaagagacggtgcattttttttaaagcttcccactgaatgtttgagatgattccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTC

Basic information

species Physcomitrella patens
transcript PP1S9_141V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_141V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA02G01060.2 (Glycine max), 3'ss of exon 10
gtgacattcgtgttcttttaagtaggcgcgaatcacctaaaaattttagaattaggattaggttaattttctagctaatcatcataataatttcgtgcgcagaagggaacctggaggctggccagactctaattcagaagagacggtgcattttttttaaagcttcccactgaatgtttgagatg-attccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTC
                                                                                             | | |     |  ||||    | |  |   |  ||   |  ||        |    | |||||||     |    |      ||   | ||| |||  ||  ||||||| ||||| ||||||||||| || || || ||||| |||||||| |||||||| || ||  | || || |||||||| ||||| || ||||||||||
---------------------------------------------------------------------------------------------catccatttgaaagaactataatgaagcttaatcttgcaaccactttttttgtcttaatttttttgggtat----aaaagtagtgcaatatgtattgtttctagGTACTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC

upper sequence: PP1S9_141V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G27810.1 (Glycine max), 3'ss of exon 10
gtgacattcgtgttcttttaagtaggcgcgaatcacctaaaaattttagaattaggattaggttaattttctagctaatcatcataataatttcgtgcgcagaagggaacctggaggctggccagactctaattcagaagagacggtgcattttttttaaagcttcccactgaatgtttgagatg-attccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTC
                                                                                             | | |     |  ||||    | |  |   |   |   |  ||        |    | |||||||      |   | |  | ||   | ||| |||  ||  |||| || ||||| ||||||||||| || || || ||||| |||||||| |||||||| || ||  | || || |||||||| ||||| || ||||||||||
---------------------------------------------------------------------------------------------catccatttgaaagaactataatgaagcttaattttgcaaccactttttttgtcttaatttttttggg---tataaatata-gtgcaatatgtattgtttctagGTTCTTAATGCAAAACCAGAAAATGTTGAGAGGGAAGCAGAAATTGTAGCACAGAGTGGTCGTCTTGGGGCAGTGACAATTGCTACCAATATGGCTGGTC

upper sequence: PP1S9_141V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 3'ss of exon 10
gtgacattcgtgttcttttaagtaggcgcgaatcacctaaaaattttagaattaggattaggttaattttctagctaatcatcataataatttcgtgcgcagaagggaacctggaggctggccagact-ctaattcagaagagacggtgcattttttttaaagcttcccactgaatgtttgagatgattccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTC
                                                                                      ||| ||  ||         |   ||   |   | |||| ||| |||  ||  || |  || || ||        |    |   |   ||| |         ||  ||  |||| || |||||||||||||| || || || |||||||| ||||||||||||||||| || ||  | || || || ||||| ||||| || ||||| ||||
---------------------------------------------------------------------------------atgctatatttatgtttctcttttgctgccaaca---tagccaaactactatatctaaatattcgttgtat-------gagatatattaactaatatc------atttaattaaagGTTCTCAATGCGAAACCAGAGAATGTAGAGAGAGAAGCAGAAATTGTTGCACAGAGTGGTCGTCTTGGGGCAGTTACAATTGCTACCAATATGGCAGGTC

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|162257358|gb|FC433441.1|FC433441
EST:     AAAGCGAATCACTCTCTGCACAGCTAACTGAAGCGTCAATTCCACATCAG                         GTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCA
genomic: AAAGCGAATCACTCTCTGCACAGCTAACTGAAGCGTCAATTCCACATCAGgtgacattcg ... ttccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCA
EST: gi|162163004|gb|FC338394.1|FC338394
EST:     AAAGCGAATCACTCTCTGCACAGCTAACTGAAGCGTCAATTCCACATCAG                         GTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCA
genomic: AAAGCGAATCACTCTCTGCACAGCTAACTGAAGCGTCAATTCCACATCAGgtgacattcg ... ttccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCA
EST: gi|162172365|gb|FC348306.1|FC348306
EST:     AAAGCGAATCACTCTCTGCACAGCTAACTGAAGCGTCAATTCCACATCAG                         GTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCA
genomic: AAAGCGAATCACTCTCTGCACAGCTAACTGAAGCGTCAATTCCACATCAGgtgacattcg ... ttccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacggtgcattttttttaaagcttcccactgaatgtttgagatgattccttgcagGTACTGAATGCGAAACCAGAAAACGTCGAAAGAGAAGCTGAAATTGTTGCACAGAGCGGGCGCTTAGGAGCCGTGACAATAGCTACGAACATGGCTGGTC
                                             ttccttgc  CT-rich tract
        attttttttaaagctt  TA-rich tract