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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG

Basic information

species Oryza sativa
transcript LOC_Os09g36710.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G138128_T03 (Zea mays), 3'ss of exon 3
tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataa--attgc--acagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
|||  ||      ||      |        | ||| |   ||       |  ||    ||  | |   | ||| | ||   | ||||| |    || |  | |||||||||| ||||| || |||||||||||| |||||||||||||| ||||||||||||| ||  |||| ||||||||||| || || |||||||||||||
tgtacttaaaaggtgatttagcctctccccgatatcttcctggccc--ctgggagcaattcagcccc-ctattccaga-atattgacaaagctgttactgatagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGATGGTCTCCGGGAACTTGAGGAGGCTGAGATTGATGAATATGTTGCTG

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G042604_T01 (Zea mays), 3'ss of exon 2
tgtctttggcctatgccactacgctagtatggtatttggttgc--atttatttagattgtttttgtcaagc----aattactgacgaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
             |   | | | || || |  |||   | |||   ||||||||| |  ||| | |||||      | || |||| |||||||| |   ||   |||||||||| ||||| || |||||||||||| |||||||||||||| ||||||| ||||| ||  ||||||||||| |||| || || || || ||||| |
--caaaaatttcttaatatttctcttgtgtt-tatgccgctgcctgtttatttagttcatttct-tcaagttccggaatattgacaaactgaca-atcctgt-tagGTTGTTGAAAGTGGTGGGAAGAACATCGAGGTTGCAGTGATGACAAAGAAGGACGGTCTCCGGGAACTCGAGGAGTCTGAGATTGATGAGTACGTTGCCG

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G51260.2 (Arabidopsis thaliana), 3'ss of exon 2
-----tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
     |    ||||  |||     ||    ||  |  |        |||    |   | | |   |||| ||| |  |       ||  ||  |  |||   ||||||||||||||||| ||||||||||| ||| |||| || |||||||   |||| |                                             
actaattgagttggattataatgttagatgagcttacttagcaaacgcacaagtagtggtggaacttgtaaagaagctg-----aaaaggatttgcattttgcagGTTGTTGAGAGTGGGGGAAAGAACATTGAGGTTGCTGTAATGACACGAGAGGAAG---------------------------------------------

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G51260.1 (Arabidopsis thaliana), 3'ss of exon 2
-----tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTC---GCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
     |    ||||  |||     ||    ||  |  |        |||    |   | | |   |||| ||| |  |       ||  ||  |  |||   ||||||||||||||||| ||||||||||| ||| |||| || |||||||   |||| ||| |||     ||||| || || |  ||||| ||      ||| |   
actaattgagttggattataatgttagatgagcttacttagcaaacgcacaagtagtggtggaacttgtaaagaagctg-----aaaaggatttgcattttgcagGTTGTTGAGAGTGGGGGAAAGAACATTGAGGTTGCTGTAATGACACGAGAGGAAGGTGTTCTGAAGCAACTAGAAGAAGAAGAAATTGATATCATTGTGG---

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G66140.1 (Arabidopsis thaliana), 3'ss of exon 2
tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataaa--ttgca---cagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGA---TGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
 ||   || ||| |    |    ||||  || ||||| |||     | |   |||| ||| |     |  || |  |  |   ||| ||     |||||   ||||| ||||||||||||||||||||||| ||| |||| || ||||||| | ||||   ||| || ||||| || || || |||||||| || | |   || |   
-gttggtgccctct----ccgtcctagc-tgatattttgtta----tttcaggattttttgtcctttgagatcatagctgttttgatatcggctttgcattgcagGTAGTTGAGAGTGGCGGAAAGAACATTGAGGTTGCCGTAATGACACGGGAGGAAACTGGGCTGCGCCAGCTAGAAGAAGCTGAAATTGATGCAATCGTGG---

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv03s0038g02300.t01 (Vitis vinifera), 3'ss of exon 2
tgtctttggcctatgccactacgct-agtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaac--tgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
      || || |    |    | | | |    ||  |  |  |   |  || | || ||||  ||   |  |  ||   ||    ||   |   |   | |||||||||||||||| ||||| ||||| |||||||| ||||||||  |  || ||||  | || ||||| || || ||||| || || |    ||||||||
--atcatgtccaagaaaagcctgtttaattctataacttatccctcatggtt-gcttcttttgatctgactttagcttttgagtcatgttttgcttcaaatagGTTGTTGAGAGTGGGGGAAAAAACATAGAGATTGCCGTGATGACGAAAGAGCATGGATTGCGGCAACTTGAAGAAGCTGAGATTGATGCCATTGTTGCTG

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0023g03690.t01 (Vitis vinifera), 3'ss of exon 2
tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaa-gcaattactgac--gaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
||   | |  | |    | |    | ||||| |  || ||  ||||| | ||  ||| |||    |    || |  || |  |   |  | ||        |||| ||||||||||| ||||||||||| || ||||| ||||||||   | || ||||||| || ||||| || ||||||||||| || |    ||||||||
tggggtag--cgagttgagtgatttggtatgatggtttgt-acatttgtatatcttgatttcagaagcataacttttggcatgtgttatcttattacatgtagGTGGTTGAGAGTGGAGGAAAGAACATAGAAATTGCTGTGATGACGAGGGAGCATGGTCTGCGGCAACTTGATGAGGCTGAAATTGATGCCATTGTTGCTG

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|86544354|gb|CI184560.1|CI184560
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86602561|gb|CI264889.1|CI264889
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88547653|gb|CI477965.1|CI477965
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86534553|gb|CI174759.1|CI174759
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86416438|gb|CI030449.1|CI030449
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|29671436|gb|CB667711.1|CB667711
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88513330|gb|CI440836.1|CI440836
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|87018143|gb|CI275957.1|CI275957
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|24468748|gb|CA305697.1|CA305697
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88239972|gb|CI239134.1|CI239134
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|112785395|gb|EE590608.1|EE590608
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGAATGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88986574|gb|CI033717.1|CI033717
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88487896|gb|CI425167.1|CI425167
EST:     AGACCTGTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTG-CGGANAAGAACATCGAGATTGCAGTGATGACACAGAA
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGA-AAGAACATCGAGATTGCAGTGATGACACAGAA
EST: gi|87007613|gb|CI281077.1|CI281077
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88240038|gb|CI239200.1|CI239200
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88239731|gb|CI238893.1|CI238893
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88207328|gb|CI207177.1|CI207177
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|87034502|gb|CI189126.1|CI189126
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86512350|gb|CI154983.1|CI154983
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88508530|gb|CI436036.1|CI436036
EST:     AGACCTGTGGCAAAGAGACCATCAAGCTCCCAATCCGTGCTGTCCTTGAG                         GTTGTTGAGAGTGGCGGAAANAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86522871|gb|CI163077.1|CI163077
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86855443|gb|CI266972.1|CI266972
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86489942|gb|CI132575.1|CI132575
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88469433|gb|CI406704.1|CI406704
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88226452|gb|CI226368.1|CI226368
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88322799|gb|CI545505.1|CI545505
EST:     GTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: GTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|87026416|gb|CI252370.1|CI252370
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88212199|gb|CI211839.1|CI211839
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|86527684|gb|CI167890.1|CI167890
EST:     AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: AGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
EST: gi|88428311|gb|CI562577.1|CI562577
EST:     TGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAG                         GTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG
genomic: TGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAG

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 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 72 (downstream exon)
Score: 20

GGGGAGGAACTCCAACTCCATGAGGGAGTTCTTGGAGAAGAATTACAAGGAGACCTCTGGCAAAGAGACCATCAAGCTCGCAATCCGTGCTCTCCTTGAGgtattttttg ... aattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttagattgtttttgtcaagcaattactgacgaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG
        attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttggcctatgccactacgctagtatggtatttggttgcatttatttagattgtttttgtcaagcaattactgacgaactgacataaattgcacagGTTGTTGAGAGTGGCGGAAAGAACATCGAGATTGCAGTGATGACACAGAAGGATGGTCTTCGCCAACTCGAGGAGGCTGAAATCGACGAATATGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - ctatgcc
- - - - - - - - - - - - - - - - - - tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttactga