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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC

Basic information

species Oryza sativa
transcript LOC_Os08g02330.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G036634_T01 (Zea mays), 3'ss of exon 13
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |   |   ||||  || ||   |      |  ||| |  ||  ||||| |||| |||  |  || | ||||| ||||||||| |||||| ||| |||| ||||| |||||  ||||||||||||||||||| ||||||||||||||||| |||||||| || || |||||
gtaatatatccatatccaaccagatttcaattt-gcttactttgtgtaatgaatctactgttcattgggtaatgaacatccatgttccagAGGGTGCAAGGGTTGCTCTGAATCTGTCAGGAACTGTGCTCAGATATTATCCTGTCAGGGTTCTGCCATCAAAAACTGCCATTGCACCAGTCAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G349794_T01 (Zea mays), 3'ss of exon 5
-----------gtaagtggtcgagtgataatta----agcatatact-tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |  ||   | ||     |  || |    | |||| | |||  || |  | | ||||  |  ||    |||| |||||||||||||||| ||| |||| |||| | |||||||||||||||||||||  || || || ||||||||||| |||||||| || ||   |||
gtaatatatccatatccaaccatgtttcagtttgcttactatgtgtaatggatctacagtttatcgagtgaaaaacatcgatgtccaagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAAACATGCTTGGATATTATCCTGTCAATGTTCTACCGTCAAAAACTGCCATTGCACCAGTCAATGAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G132286_T01 (Zea mays), 3'ss of exon 3
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |   |   ||||  || ||   |      |  ||| |  ||  ||||| |||| |||  |  || | ||||| |||||||||||||||||||| |||| |||||  |||| |||||||||||||||||||| ||||||||||||||||| |||||||| || || |||||
gtaatatatccatatccaaccagatttcaattt-gcttactttgtgtaatgaatctactgttcattgggtaatgaacatccatgttccagAGGGTGCAAGGGCTGCTCTAAATCTGTCAGGAACTATGCTCGGATATTATCCTGTCAGGGTTCTGCCATCAAAAACTGCCATTGCACCAGTCAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G175541_T02 (Zea mays), 3'ss of exon 4
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||    |||| |||||||||||||||| ||| ||||  |||||||||||||||||||||||||||  || ||||| ||||||||||| |||||||| || |||  |||
gtaatatatccatatacaaccatgtttcagttt-gcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcctagAGGGTGCAAGGGCTGCTCTGAATCTGTCAAGAACCGTGCTTGGATATTATCCTGTCAATGTTCTGCCGTCAAAAACTGCCATTGCACCAGTCAACAAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G014573_T01 (Zea mays), 3'ss of exon 2
-----------gtaagtggtcgagtgataatta----agcatatact-tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |  ||   | ||     |  || |    | |||| | |||  || || | | ||||  |  ||   ||||| |||||||||||||||| ||| |||| |||| |||||||||||||||||||||||  || || |||||||||||||| |||||||| || |||  |||
gtaatatatccatatccaaccatgtttcagtttgcttactatgtgtaatggatctacagtttatcgggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAAACGTGCTTGGATATTATCCTGTCAATGTTCTACCATCAAAAACTGCCATTGCACCAGTCAACGAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G161649_T01 (Zea mays), 3'ss of exon 2
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |   |   ||||  || ||   |      |  ||| |  ||  ||||| |||| | |  |  || | ||||| |||||||||||||||| ||| | || ||||| ||||| |||||||||||||||||||| ||||||||||||||| | |||||||| || || |||||
gtaatatatccatatccaaccagatttcaattt-gcttactttgtgtaatgaatctactgttcattgggtaatgaccatccatgttccagAGGGTGCAAGGGCTGCTCTGAATCTATCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCAAAAACTACCATTGCACCAGTCAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G457231_T01 (Zea mays), 3'ss of exon 6
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC-
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||   ||||| ||||||||||||| || ||| |||| ||||||||||||||||||||||||||||  || ||||| |||||| |||| |||||||| || ||   ||| 
gtaatatatccatatccaaccatgtttcagttt-gcttactctgtgtaatggatctactgtttatcgggtga-aaacatcgatgtcccagAGGGTGCAAGGGCTGCCCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTGTCAATGTTCTGCCGTCAAAA-CTGCCATTGCACCAGTCAAAGAAACA

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G069102_T01 (Zea mays), 3'ss of exon 4
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||   ||||| ||||||| |||||||| ||| |||| |||||||||||||||||||||||||||| ||| ||||| ||||||||||| |||||||| || |||  |||
gtaatatatccatatcccaccatgtttcagttt-gcttactctatgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccagAGGGTGCAAGAGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTGTCAAGGTTCTGCCGTCAAAAACTGCCATTGCACCAGTCAACGAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G173428_T02 (Zea mays), 3'ss of exon 3
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |   |   ||||  || ||   |      |  ||| |  ||  ||||| |||| |||  |  || | ||||| |||||||||||||||| ||| |||| ||||| ||||| |||||||||||||||||||| |||||||| |||||||| |||||||| || || |||||
gtaatatatccatatccaaccagatttcaattt-gcttactttgtgtaatgaatctactgttcattgggtaatgaacatccttgttccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACTGTGCTCGGATATTATCCTGTCAGGGTTCTGCCATCGAAAACTGCCATTGCACCAGTCAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G376619_T01 (Zea mays), 3'ss of exon 5
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC-------------------------------------------------------------------------------------
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||   ||||| |||||||||||||||| ||| |||| |||||||||||||||||||||||| |||  || || || ||||||||||| |||||||| || |||  |||                                                                                     
gtaatatatccatatccaaccatgtttcagttt-gcttactctgtgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccagagggtgcaagggctgctctgaatctgtcaggaaccgtgcttggatattatcctatcaatgttctaccgtcaaaaactgc-attgcaccagTCAACGAAACATTCCTACCCAGGGTATGCAAACCTTCCGGAACCAACATGCTTGTCTTAAGTTCATGGCTCAATGTTCATGCTCTATCTGATATG

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G398795_T01 (Zea mays), 3'ss of exon 6
gtaagtggtcg-agtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
||  |   ||  || | | | | |  |      || ||| |||  |||     |   |   |||| | ||       ||| || || |   |||  | ||  | |||           |   |    ||    | |||||  ||  || |||  |     | || |        
gtttgctttcatagagttcactgatgagggtaatatatccatatccaaccatgtttcagTTTGCT-TACTCT-----GTGTAATGGGTCTACTATTTATGGGGTGAAAAACATCGATGTCCCAGAGGGTGCAAGGGCTGC--TCTGAATCTGTCAGGAACCGTGCTT-------

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G044246_T02 (Zea mays), 3'ss of exon 4
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||   ||||| |||||||||||||||| ||| |||| |||||||||||||||||||||||| |||  || ||||  ||||||||||| |||||||| || |||  |||
gtaatatatccatatccaaccatgtttcagttt-gcttactctgtgtaatggatctactgtttatggggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGTGCTTGGATATTATCCTATCAATGTTCTGCTGTCAAAAACTGCCATTGCACCAGTCAACGAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G456149_T01 (Zea mays), 3'ss of exon 6
-----gtaagtg-gtcgagtgataattaagcata--tact--------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
      ||      || |   ||  || |   ||  ||||        | |||| |  ||  || || | | ||||  |  ||   ||||| |||||||||||||||| ||| |||| ||||||| ||||||||||||||| ||||  || ||||| ||||||||||| |||||||| || |||  |||
gtaatatatccatatccaacaatgtttcaatttacttactctgtgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCTGAATCTGTCAGGAACCGAGCTTGGATATTATCCAGTCAATGTTCTGCCGTCAAAAACTGCCATTGCACCAGTCAACGAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G166091_T01 (Zea mays), 3'ss of exon 6
-----------gtaagtggtcgagtgataattaagcatatact------tagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
            ||      |  ||   | ||  || ||  ||      | |||| |  ||  || || | | ||||  |  ||   ||||| |||||||||||||||  ||| ||||  |||||||||||||||||||||||||||  || ||||| ||||||||||| |||||||| || |||  |||
gtaatatatccatatccaaccatgtttcagttt-gcttactctgtgtaatggatctactgtttatcgggtgaaaaacatcgatgtcccagAGGGTGCAAGGGCTGCTCCGAATCTGTCAAGAACCGTGCTTGGATATTATCCTGTCAATGTTCTGCCGTCAAAAACTGCCATTGCACCAGTCAACGAAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G40760.1 (Glycine max), 3'ss of exon 6
gtaa-gtggtcgagtgataatt--aagcatatacttag-atcaatagtcaattg-gttaataaactgctctgct-gcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
||||  ||  |     ||  ||  ||   | || ||   ||  | | |    ||  |||| |   || | |||| |||||  |||||||||||||| | ||  |||| |||||| ||||||||||||| ||  | || || || || || |||||||| ||||| |||||||| |||||
gtaacatgaccaccaaatgtttgcaactttgtaattgttattgacatttctctgtattaacag--tgttgtgcttgcagATGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTACTACCTTCGAAAACTGCTATTGCCCCTGTTAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G35640.1 (Glycine max), 3'ss of exon 5
gtaa-gtggtcg--agtgataattaagcatatacttag-atcaatagtcaattg-gttaataaactgctctgc-tgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
||||  ||  ||  |    ||   |    | |  |||  || || | |  | ||  |||| |   || | ||| || |||  |||||||||||||| | ||  |||| |||||| ||||||||||||| ||  | || ||||| || ||||||||||| ||||  |||||||| |||||
gtaacatgaccgccaaatgtatgcatctttgtgattattattaacatttcactgtattaacag--tgttgtgcctgtagAAGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTGCTACCTTCAAAAACTGCTATTGTCCCTGTTAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G14030.2 (Glycine max), 3'ss of exon 6
gtaa-gtggtcg--agtgataattaagcatatacttag-atcaatagtcaattg-gttaataaactgctctgc-tgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
||||  ||  ||  |    ||   |    | |  |||  || || | |  | ||  |||| |   || | ||| ||||||  |||||||||||||| | ||  |||| |||||| ||||||||||||| ||  | || ||||| || ||||||||||| ||||| |||||||| |||||
gtaacatgaccgccaaatgtatgcatctttgtgattattattaacatttcactgtattaacag--tgttgtgcctgcagAAGGTGCAAGGGCTGCTTTGAACCTGTCTGGAACCATGCTTGGATATTACCCGTTGAGAGTGCTACCTTCAAAAACTGCTATTGCCCCTGTTAATCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G10610.2 (Arabidopsis thaliana), 3'ss of exon 4
-----gtaagtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgc---tctg----ctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
      | |||       ||  |  |    ||    | |   |  ||     |||||| ||    ||    | ||     || || | |||||||| ||||||| |||||||| || ||  |||||||||  |||||||| | |||  |||| || || || || |||||||| |||||||||||
gtatcattagtttctctatgtaatctgtttattggataatgcctgtaagtgcttggtttatggtttgtcattttgggacttgtagTGGGTGCAAGGACTGCTCTGAATTTGTCTGGGACGATGCTTGGATTCTATCCTGTGAAGGTTATGCCGTCTAAGACAGCTATTGCACCGGTTAACCCAAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0025g02740.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtggtcgagtgat---aattaagcata-tacttagatcaatagtc---aattggttaataaact------gctctgct---gcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
||||||  |  | | |    ||||    ||  | | ||  |||   ||      ||| ||| |  |||        | || |   |||||  ||||| |||||||| | | | || | || ||  |||||||||| || ||||| |||||||||||||| ||||| || |||||||| |||||||| ||
gtaagtaattaacttacctaaattctatatggtgcataattcacaggtttttggttgtttatttgactctgggtattttggttatgcagAAGGTGCACGGGCTGCTTTGAGTCTGGCAGGGACAATGCTTGGATACTACCCTGTGAGGGTGCTGCCATCTAAAACAGCCATTGCACCAGTTAACCCTAC

upper sequence: LOC_Os08g02330.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0098g01040.t01 (Vitis vinifera), 3'ss of exon 5
-------------------gtaagtggtcgagtgataattaagcatatacttagatcaatagtcaatt----ggt-taataaactgctctgc---tgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
                   ||     || |  ||      | ||||   |||   | || | |   ||    ||| |||| |||     ||    ||||||  | ||  |||||||||| | |||| |||||||  ||||||| |||||||| || || ||||| || ||||||||||| ||||||||||||||||||||
acattaaattggtttaaccgttgaccgttgtatgtagcgcatgcatcctcttgcctgaacattgtttttttaggtataattaacattcatgtgcttgcagAAGGCGCGCGGGCTGCTCTGAGTTTGGCGGGAACAATGCTTGGGTATTATCCAGTGAGAGTGCTACCTTCAAAAACTGCAATTGCACCTGTTAACCCAAC

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|86899176|gb|CI298078.1|CI298078
EST:     TTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: TTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|29646834|gb|CB651841.1|CB651841
EST:     GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|29643786|gb|CB648793.1|CB648793
EST:     GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|29646833|gb|CB651840.1|CB651840
EST:     GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
genomic: GGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATC
EST: gi|218493611|gb|FG968673.1|FG968673
EST:     GATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTNGATGAGG                         AGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTAT
genomic: GATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACT-GATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTAT

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: 48 (upstream exon), 71 (downstream exon)
Score: 82

GTTGTGGACTGTCGTATGTGTGGGGATCCGAATTCTGTTCTTCGTTTTGCTTTCATAGAGTTCACTGATGAGGgtaagtggtc ... tctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC
                               ggttaat  putative branch site (score: 82)
                                         ctgctct  putative PPT
                           aattggttaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtggtcgagtgataattaagcatatacttagatcaatagtcaattggttaataaactgctctgctgcagAGAGTGCAAGGGCTGCTCTAAATTTGTCGGGAACCGTGCTTGGATATTATCCTGTCAGGGTGCTGCCATCAAAAACTGCGATTGCACCTGTTAACCCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC