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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattagcattagataacacttgtgttgtgccatttttatcgtattattttactgtatgaggtgcattattttgactcaatactgtcgcttccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGTGGAGTGCTCTCTGGAACTGCAG

Basic information

species Oryza sativa
transcript LOC_Os09g24690.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24690.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G166963_T01 (Zea mays), 3'ss of exon 2
gattagcattagata-acacttgtgttgtgccatttttatcgt-attattttactgtatgaggtgcattattttgact--caatactg---tcgcttccatttt--cagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGTGGAGTGCTCTCTGGAACTGCAG
           |||  |   |  |||| | | ||||   |  | |||| ||  |||| |  ||    | || |||  |    | || |   | | || ||||||  |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||||||||
--------gaggatgcatgttcatgttctacaatttgccttattattacttgtctgtgtt-ggcagttcatcttggttgctcacaccgagatggttttcattttttcagATTCCCCATCTGAGGCCAGCTGAGTACAAAAGGTCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGGGGAGTACTATCTGGAACTGCAG
















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|88975429|gb|CI023680.1|CI023680
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88902392|gb|CI087930.1|CI087930
EST:     TGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTNGTCTAGGAAC
genomic: TGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88961791|gb|CI096951.1|CI096951
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86482848|gb|CI125481.1|CI125481
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|55435797|gb|CV731034.1|CV731034
EST:     CGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: CGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|27576721|gb|CA999415.1|CA999415
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|33690860|gb|CF319099.1|CF319099
EST:     AGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88212826|gb|CI210677.1|CI210677
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|87016834|gb|CI284168.1|CI284168
EST:     AGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAANGAAGATCCAGNGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAA
genomic: AGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAA-GAAGATCCAG-GGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAA
EST: gi|86596546|gb|CI284857.1|CI284857
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|58668332|gb|CK057018.1|CK057018
EST:     AGAGGGCGAGCGGACCAAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86257931|gb|CI064284.1|CI064284
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88955852|gb|CI092141.1|CI092141
EST:     GCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTNGTCTAGGAAC
genomic: GCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|87033868|gb|CI188492.1|CI188492
EST:     AGAAGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86533492|gb|CI173698.1|CI173698
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88209963|gb|CI209812.1|CI209812
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86532768|gb|CI172974.1|CI172974
EST:     AAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGTTTGTCTAGGAAC
genomic: AAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|87032333|gb|CI264114.1|CI264114
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|89165100|gb|CI255157.1|CI255157
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86532764|gb|CI172970.1|CI172970
EST:     GGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATTCAGGTTGTCTAGGAAC
genomic: GGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88207178|gb|CI207027.1|CI207027
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|33669976|gb|CF298215.1|CF298215
EST:     GGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: GGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88213746|gb|CI213595.1|CI213595
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88211494|gb|CI211134.1|CI211134
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88237022|gb|CI236871.1|CI236871
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88224604|gb|CI222784.1|CI222784
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|58589260|gb|CF987568.1|CF987568
EST:     AGAGGGCGAGCGGACCAAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCGGAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86597221|gb|CI280358.1|CI280358
EST:     GAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGAACCAGGTTGTCTAGGAAC
genomic: GAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|29686974|gb|CB683249.1|CB683249
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAATAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|38480922|gb|CF965011.1|CF965011
EST:     AGAGGGCGAGCGGACCAAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACGAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|10930619|gb|AU160893.1|AU160893
EST:     GAGGGCGAGCGGGCCCAAGTGNCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: GAGGGCGAGCGGGCCCAAGTG-CCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|55441850|gb|CV734251.1|CV734251
EST:     CCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTTTAGGAAC
genomic: CCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88207013|gb|CI206862.1|CI206862
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|33815301|gb|CF333502.1|CF333502
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|44676042|gb|CR289476.1|CR289476
EST:     GGGAAGAATATCCA-GGA                         T
genomic: GGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcag-
EST: gi|44676042|gb|CR289476.1|CR289476
EST:     GGGAAGAATATCCA-GGA                         T
genomic: GGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcag-
EST: gi|88212873|gb|CI210724.1|CI210724
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|11172025|gb|AU164079.1|AU164079
EST:     AGA-GGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|33669977|gb|CF298216.1|CF298216
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|86533592|gb|CI173798.1|CI173798
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTATCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|10931469|gb|AU161743.1|AU161743
EST:     CCCGTGACCCGGGAAGAAGATCCAGGGA                         ATTCCNCGNTCTCAAGGGCCTGCTGAGTCACAAGAGATCCAGGTTGTCTA-
genomic: CCCGTGA-CCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCC-CCATCTC-A-GGCCTGCTGAGT-ACAAGAGATCCAGGTTGTCTAG
EST: gi|88208657|gb|CI208506.1|CI208506
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATCCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
EST: gi|88211936|gb|CI211576.1|CI211576
EST:     AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGA                         ATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC
genomic: AGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAAC

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: 73 (upstream exon), 74 (downstream exon)
Score: 101

GTGGCAAGCTCGTGTACCAGTACACCAAGAAGAGGGCGAGCGGGCCCAAGTGCCCCGTGACCGGGAAGAAGATCCAGGGAgtgagtgcct ... ccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGTGGAGTGCTCTCTGGAACTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttactgtatgaggtgcattattttgactcaatactgtcgcttccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGTGGAGTGCTCTCTGGAACTGCAG
                       ttttgac  putative branch site (score: 101)
                                       tcgcttccattttc  putative PPT
                   attattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattagcattagataacacttgtgttgtgccatttttatcgtattattttactgtatgaggtgcattattttgactcaatactgtcgcttccattttcagATTCCCCATCTCAGGCCTGCTGAGTACAAGAGATCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGTGGAGTGCTCTCTGGAACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - tgtgttg
- - - - - - - - - - - - - -tgccatt
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcgct