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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTGAACTTCTTCCAGCACATATTTCAGAAGGGATAAGGGTTATTCCTCCCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacagcatctcccaccttgatcattgattcttatcatcaattttttgccacttaagttttactagttgctgacttgatcaaattttag

Basic information

species Oryza sativa
transcript LOC_Os04g57210.3
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57210.3 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G043862_T01 (Zea mays), 5'ss of exon 11
CCGTGAACTTCTTCCAGCACATATTTCAGAAGGGATAAGGGTTATTCCTCCCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacagcatctcccaccttgatcattgat-tcttatcatcaattttttg--ccacttaagttttactagttgctgacttgatcaaattttag
 |   ||||||||||| |  |||| |||||||| ||||| ||  | || ||  |||||||||| ||||||||||||||||||||||| ||||| |||||||||||||||     |   |||| |||  || || | | |   | |||||  |    |   | | ||| |||   |  ||   || |  || |||||
TCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggaca-----tgaaacctcgattttttatgtgtcaaatttaatttcatcattcgtgttaatttcacttactagtg-tctgctttaactttag
















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|87033311|gb|CI187935.1|CI187935
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTCTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|33686736|gb|CF314975.1|CF314975
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29626709|gb|CB631720.1|CB631720
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88549085|gb|CI478941.1|CI478941
EST:     AAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: AAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88480903|gb|CI418174.1|CI418174
EST:     TGGTGCACAAATGATTAGCCAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: TGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|5005297|gb|AU070459.1|AU070459
EST:     CAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29632995|gb|CB638004.1|CB638004
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29663904|gb|CB660179.1|CB660179
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88503568|gb|CI431074.1|CI431074
EST:     GGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: GGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29663905|gb|CB660180.1|CB660180
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29618214|gb|CB623226.1|CB623226
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88473694|gb|CI410965.1|CI410965
EST:     GATTCTGCCTGGTTTGGTGCAAAAATGATTAGCGAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: GATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88489921|gb|CI427193.1|CI427193
EST:     ATGATTAGCAAC                         GTGGGCACTTTCACGGAGGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCA
genomic: ATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGA-GGCATGGTGCATCAAGAAGAAGCAGTTTCGCCA
EST: gi|29626176|gb|CB631187.1|CB631187
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88273743|gb|CI394149.1|CI394149
EST:     AAAATGATGAGCGAC                         GTGAGCACTTTCACGGAGGCAT-GTGCATCAAGAAGAAGCCAGTTTCGCCA
genomic: AAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAG-CAGTTTCGCCA
EST: gi|89196232|gb|CI397234.1|CI397234
EST:     AAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: AAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29679980|gb|CB676255.1|CB676255
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29624048|gb|CB629059.1|CB629059
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88478221|gb|CI415492.1|CI415492
EST:     ATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: ATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|58589122|gb|CF987430.1|CF987430
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCAT
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCAT
EST: gi|29671067|gb|CB667342.1|CB667342
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88481364|gb|CI418635.1|CI418635
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCCNAAATGATTAGCNAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|7332570|gb|AU085916.1|AU085916
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29663603|gb|CB659878.1|CB659878
EST:     CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88518647|gb|CI446301.1|CI446301
EST:     CCGATTCTGCCTTGTTTNGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|29679981|gb|CB676256.1|CB676256
EST:     CCCCATTTGGCACCGATTTTGCCTGGTTTGGTGCAAAAATGATTAGCAAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: CCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
EST: gi|88524583|gb|CI450511.1|CI450511
EST:     ATGATTAGCCAC                         GTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG
genomic: ATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAG

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: 66 (upstream exon), 75 (downstream exon)
Score: 51

CCGTGAACTTCTTCCAGCACATATTTCAGAAGGGATAAGGGTTATTCCTCCCCCATTTGGCACCGATTCTGCCTGGTTTGGTGCAAAAATGATTAGCAACgtaaggacag ... caaattttagGTGAGCACTTTCACGGAGGCATGGTGCATCAAGAAGAAGCAGTTTCGCCAGAAGACTCGTCGCAATGGTCCATCTTTTGTGAATGTGTGGTAATAGAGCC




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