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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtaaactctgtttcagtctgttaattgcgatgaccagttgccgcttaaatccctttttattgaagttggagctgctgttttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA

Basic information

species Oryza sativa
transcript LOC_Os05g01700.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G060045_T01 (Zea mays), 3'ss of exon 22
gtcagtgtaaactctgtttcagtctgttaattgcgatgaccagttgccgcttaaatccctttttattgaagttggagctgctgttttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA
||| || | ||||  |    ||    |  |||    ||  |  ||  || |  |  | || || | ||||     |    ||   || |   |||| |||||||||||||| |||||||| |||||||| || ||||| ||||| ||
gtcggtattaact--ggcagagcacatctatt----tgttcctttttcgttctatacgctattaagtgaaaagtcaatctcttccttttgctagGCTCGTTTGTTTTTCCATCATCCTAAGTTTGGTATCCTGGACGAGTGCACCAA

upper sequence: LOC_Os05g01700.1 (Oryza sativa), 3'ss of exon 20
lower sequence: PP1S105_6V6.1 (Physcomitrella patens), 3'ss of exon 26
-------------------------------------------------------------------------------------gtcagtgt-----aaactctgtttcagtctg-ttaat-tgcgatgac-cagttgccgctta-aatccctttttattgaagttggagctgctgttttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA
                                                                                      |   |||     | | | | ||  ||  || || || |||  |||| || | |    ||| ||    ||| |     | |||  ||||||  |      ||||| ||  |||| |||||||||||||| ||||| ||||||||||| ||||||||
gtgagttcaggaattggaaatggcaaagctgcgttgggatcggaaatagatgacgagagtcttaaattagacgcttcattcatctatttatgtttgaaagattgtattcgagaatgattgatctgcagtgactcactggttatttacaaggaatttctcacttatttgtggctgctcgtca---acagGCACGACTGTTCTTCCACCATCCTAAGTTTGGGATTCTTGACGAGTGCACGAA
















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|88995965|gb|CI037256.1|CI037256
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|86437286|gb|CI119008.1|CI119008
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|88985767|gb|CI033096.1|CI033096
EST:     ACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: ACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|86251544|gb|CI016833.1|CI016833
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|88975781|gb|CI024032.1|CI024032
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACGATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|88254258|gb|CI352884.1|CI352884
EST:     AAGATATTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: AAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|29685003|gb|CB681278.1|CB681278
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACATCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|86902061|gb|CI300300.1|CI300300
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
EST: gi|86540220|gb|CI180426.1|CI180426
EST:     CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATG                         GCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG
genomic: CAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACG

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), 69 (downstream exon)
Score: 19

GAATGTTCGGTTGGTCTATCTTCTAGAAAGAGAAGGATGGGACTCAACTTCAAACTGGGAAGATGTTTTATCGTTGGGAGAACAGCAGAGGCTTGGGATGgtcagtgtaa ... tttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagttgccgcttaaatccctttttattgaagttggagctgctgttttcttgcagGCCCGTTTGTTTTTCCACCATCCTAAATTTGGTATTCTTGACGAATGCACGAA
                                         ctgttttctt  CT-rich tract
                    tttttattgaagtt  TA-rich tract