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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaaaaatgaatgcccaatatgcacagtactttattttgtttttatttcatttcattatacataagttgtaaaagctatttgttttttgtgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG

Basic information

species Zea mays
transcript GRMZM2G161728_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161728_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g49070.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------------aacaaaaatgaatgcccaatatgc-acagtactttattttg---tttttatttcattt-cattatacataagttgtaaaagctatttgttttttgtgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG
                                                                                ||| |    |||    |||||   ||  |||| |||||   ||   || || | |   | | |  ||   ||||||   | |||  |||    ||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||||||||| ||| | ||||||
gtaagtgcctctgttacagtgattagggcatctttttttgtatgaatacctattatgttctaatgtttccatactaatggaaagacatttgcatgttatgctgaagacctttgttttggacttcccatgtcgtctatctgaaatttagagtgtaaacaatgtttacttt----gcatttcagGTCTGCTAATATCGGAGTATTTCTTTGCTTAAAGTGTGGAGATGTACATAGAGCACTTGGACCAGACGTTTCAAAG

upper sequence: GRMZM2G161728_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT4G21160.3 (Arabidopsis thaliana), 3'ss of exon 3
----------------------------------------------------aacaaaaatgaatgcccaatatg--cacagtactttattt-tg---tttttatttcatttcattatacataagttgtaaaagctatttgttttttgtgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG
                                                    ||  |   ||| ||     ||||  |    | |  || || ||   |||||  ||  |||| || | | |||      ||| || || |||  ||    ||| ||| || |||||||||||||||||| | |||||||||||| | | ||| || ||    |||||   | | |||||||||
gtaagttttgccatttttatgttttgttccagtaagcattttatgcttctctaagcagtttgattgaatgttatgatcttgtttccctacttgtgcattttttggtttgtttcgtttttcgtaaacccataaaactcttggttgctt----attacagGTCAGCTAATATTGGAGTGTTTATATGCTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGCAGTCATATCTCAAAG
















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|74234877|gb|DT642791.1|DT642791
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211285005|gb|FL330934.1|FL330934
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|148970443|gb|EE021294.2|EE021294
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|148982152|gb|EE028182.2|EE028182
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211110591|gb|FL338760.1|FL338760
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211369326|gb|FL186711.1|FL186711
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211029006|gb|FL358137.1|FL358137
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGA                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAA
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211369327|gb|FL186712.1|FL186712
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211531455|gb|FL327595.1|FL327595
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211381172|gb|FL350978.1|FL350978
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211255468|gb|FL340105.1|FL340105
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|78079893|gb|DV508305.1|DV508305
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211230929|gb|FL338421.1|FL338421
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211342585|gb|FL343867.1|FL343867
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAAYGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211005122|gb|FL358937.1|FL358937
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|94474289|gb|EB703247.1|EB703247
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAAATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211437933|gb|FL338199.1|FL338199
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211531838|gb|FL338634.1|FL338634
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211467079|gb|FL315616.1|FL315616
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211268265|gb|FL364919.1|FL364919
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|13558576|gb|BG549932.1|BG549932
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211409281|gb|FL329226.1|FL329226
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGA
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGA
EST: gi|211430763|gb|FL360603.1|FL360603
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAAATGTGGAGATGTTCATA
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAA-TGTGGAGATGTTCATA
EST: gi|211369324|gb|FL186709.1|FL186709
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|91050811|gb|EB161229.1|EB161229
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|149008427|gb|EE040587.2|EE040587
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|71327521|gb|DR800373.1|DR800373
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211006794|gb|FL317953.1|FL317953
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211354852|gb|FL354351.1|FL354351
EST:     AGTGACAATAGGATATGTGCTGACTGTGGT-CACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211291944|gb|FL367895.1|FL367895
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211118991|gb|FL350362.1|FL350362
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211279546|gb|FL328174.1|FL328174
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|76287384|gb|DV026952.1|DV026952
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211375633|gb|FL110751.1|FL110751
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAWATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211284991|gb|FL330460.1|FL330460
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211500673|gb|FL332349.1|FL332349
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211510664|gb|FL361518.1|FL361518
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211094177|gb|FL353110.1|FL353110
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
EST: gi|211286672|gb|FL320843.1|FL320843
EST:     AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGC                         ATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG
genomic: AGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GCAAAGCAAGAAAATTGAAGGATCTCATGATAAAAAGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

GCAAAGCAAGAAAATTGAAGGATCTCATGATAAAAAGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

GCAAAGCAAGAAAATTGAAGGATCTCATGATAAAAAGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GCAAAGCAAGAAAATTGAAGGATCTCATGATAAAAAGTGACAATAGGATATGTGCTGACTGTGGTGCACCTGATCCCAAATGGGCgtaagtgacg ... tgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcatttcattatacataagttgtaaaagctatttgttttttgtgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG
                                      ttttttgt  CT-rich tract
     atttcattatacataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaaaaatgaatgcccaatatgcacagtactttattttgtttttatttcatttcattatacataagttgtaaaagctatttgttttttgtgcatttcagATCTGCTAATATTGGAGTGTTTCTTTGCTTAAAATGTGGAGATGTTCATAGGGCACTTGGACCTGACATCTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
aacaaaa
- - - - tgaatgc
- - - - - - - - - -tatgcac
- - - - - - - - - - - - - - - - - - - tgttttt