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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_Os11g28340.2
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|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

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: 64 (upstream exon), 61 (downstream exon)
Score: 32

GCTGGGTTGCGGGCATCGTGCAGACTCTCTTGTATGCTGACTTCTTCTACTATTACATAATGAGgtatttgact ... caatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATCCAAGATAGGCTAGGTAAAACTTGTTAAATAGATAGAAAGGCATGATACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcattctgctactattgttcctttccattgactactccaaacaatttgcagCTGGAAGAACAATGTGAAGCTGGAGCTACCAGCCTGAGCTCATTTTTCATCCAAGATAGGCTAGGTAAAACTTGTTAAATAGATAGAAAGGCATGATACA
                             cattgac  putative branch site (score: 32)
                                          aaacaattt  TA-rich tract