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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgacttggttttaccttatcatttcattctgctactattgttcctttccattgactactccaaacaatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATCCAAGATAGGCTAGGTAAAACTTGTTAAATAGATAGAAAGGCATGATACA

Basic information

species Oryza sativa
transcript LOC_Os11g28340.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G031802_T01 (Zea mays), 3'ss of exon 3
------gtatttgacttggttttaccttatcatttcattctgctactattgttcctttccattgacta----ctccaaacaatt-tgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCAT----CCAAGATAGGCTAGGTAAAACTTGTTAAATAGATAGAAAGGCATGATACA-
       ||  |  ||| |  | ||||    || |  || || ||| | ||| ||| || |||||  |    |||||||||||  | |||||||||||||||||||||||| ||||| ||||| | || |   |  || |    ||||||||   ||||  ||  |     |  ||||||  ||||   ||||| 
gtaactctaggttcctttggctaacctagatatctt-ttttgttacaaatgtccctctc-attgaaaatgttctccaaacaatggtacagCTGGAAGAACAATGTGAAGCTAGAGCTGCCAGCTTAAGGTTGCTGCTCCTGTCCCCAAGATATAGTAGGGTAATAT-----ATCAGATAGGCAGGCCCCATACAC

upper sequence: LOC_Os11g28340.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S29_123V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------------------------------------------gtatt--tgacttggttttaccttatcatttcattctgctactattgttcctttcca----ttgactactccaa-acaat-ttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATCCAAGATAGGCTAGGTAAAACTTGTTAAATAGATAGAAAGGCATGATACA
                                                                    || ||  |||  | |  | || |  |    |  || ||  |   |  | | |||        ||| |     ||  |  | |||||||||||||||||| | ||||||| |||||||||| |    | |      | |  ||     ||  | |  ||| ||  ||     |  ||   |   |   
gtattgacttgcaaccatcgcattcctcgcaaaggagtttgttgaaatgtttggttgcaaagtcatgcgtgttaatgatatagggtcacttctttggattcttgtgtcaaattcttacattttgggtttctgattgtgtgaatgcggtgttgcagCTGGAAGAACAACGAGAAGCTGAAGCTACCAGCTTAGATTTACGCCGAAACGTAGGGTTTCTCCGGAGCACTAGTGGAAGGTGCATCAATTTAGTGTTTG
















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|117216901|gb|CT861591.1|CT861591
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88476998|gb|CI414269.1|CI414269
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88849104|gb|CI087626.1|CI087626
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGCAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88555052|gb|CI485279.1|CI485279
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88473468|gb|CI410739.1|CI410739
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88528582|gb|CI456828.1|CI456828
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88488148|gb|CI425419.1|CI425419
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|86542052|gb|CI182258.1|CI182258
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|86529172|gb|CI169378.1|CI169378
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|426840|gb|D22915.1|D22915
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|86886118|gb|CI321154.1|CI321154
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATGACATAATGAG                         CT-GAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|27546640|gb|CA764760.2|CA764760
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88262756|gb|CI366530.1|CI366530
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGGCTGGAGCTACCAGCCTGAGCTCATTTTTCAT
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAA-GCTGGAGCTACCAGCCTGAGCTCATTTTTCAT
EST: gi|86870391|gb|CI319497.1|CI319497
EST:     TCGTGCAGACTCTCTTGTATGGCTGACTTCTTCTACTATTACATAATGAGG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCAT
genomic: TCGTGCAGACTCTCTTGTAT-GCTGACTTCTTCTACTATTACATAATGA-Ggtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCAT
EST: gi|88533140|gb|CI460677.1|CI460677
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88241404|gb|CI241253.1|CI241253
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88541507|gb|CI470782.1|CI470782
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|33691459|gb|CF319698.1|CF319698
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCCGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|86545642|gb|CI185848.1|CI185848
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88529756|gb|CI458100.1|CI458100
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|89187774|gb|CI009758.1|CI009758
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88439304|gb|CI536276.1|CI536276
EST:     ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: ATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
EST: gi|88471410|gb|CI408681.1|CI408681
EST:     CTCTTGTATGCTGACTTCTTCTACTATTACATAATGAG                         CTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC
genomic: CTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcattctgctactattgttcctttccattgactactccaaacaatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATCCAAGATAGGCTAGGTAAAACTTGTTAAATAGATAGAAAGGCATGATACA
                             cattgac  putative branch site (score: 3)
                                          aaacaattt  TA-rich tract