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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcctctcacattttgaaggcttagtcctttagtctgtaattgtctgattctaatgtgatgtcttccatcatactattcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAACAATTACCCACAGAATAAACCTGTCTTACCTGTCTAATGAAATTTAGTG

Basic information

species Oryza sativa
transcript LOC_Os02g40890.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G060870_T02 (Zea mays), 3'ss of exon 6
gtatggcctctcacatt--ttgaaggcttagtcctttagtctgtaattgtctgattctaatgtgatgtcttcca-tcatactattcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCA--TTCCTATGCAACAATTACCCACAGAATAAACCTGTCTTACCTGTCTAATGAAATTTAGTG
|||||| ||||| ||    || | |  | |||  ||| | |  |     |  |   ||  ||  ||  ||      | | |||||||||||||| || ||||| ||||||||| |||||||||| ||  ||    ||| | |     |||||  ||| ||||| | ||||||| |   || | |   |  ||  
gtatggtctctcccaccaattcaggattcagttgttttgccact-----ttcgtgccttgtgaaatagctctaggccctgctattcttgcagGCGAGCGTTGGTCTTGATGATATGAAGGCTTCGTAGAGCGATCTCCAAGGTGGTGATTACA-ACAAAATAAGCGTGTCTTATCAAACTCAAGTGTTGCAGA-

upper sequence: LOC_Os02g40890.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G125556_T01 (Zea mays), 3'ss of exon 6
gtatggcctctcacattttgaaggcttagtcctttagtc-tgtaattgtctgattctaatgtgatgtcttc------catcatactattcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTA-ATGCATTCCTATGCAACAATTACCCACAGAATAAACCTGTCTTACCTGTCTAATGAAATTTAGTG---
|||||| ||||| || ||| |||  | |||  ||| |     |   | |||  ||  |     |  |  |         ||   | |||||||||||| || || || |||||||||||||||||||| || ||  ||  | ||||    |||||  ||| ||||| | ||||||||    || |  |   ||   |   
gtatggtctctcccaattt-aagcttcagttgttttgcaacttgggtatcttgttaaacaacaactttctggtatggtctctcccaattcttgcagGCGAGCGTCGGTCTTGATGATCTGAAGGCTTCATAGATCAATCTCCATGC--TGATTACA-ACAAAATAAGCATGTCTTACGAAACTCA-AAGTGTTGCCGAGG
















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|88476057|gb|CI413328.1|CI413328
EST:     AATTCTG--CTACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88504138|gb|CI431644.1|CI431644
EST:     AATTCTG--CTACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88985226|gb|CI006880.1|CI006880
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|86600278|gb|CI356035.1|CI356035
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|89196552|gb|CI400722.1|CI400722
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACGTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCCA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88262804|gb|CI364382.1|CI364382
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|396941616|gb|HO188273.1|HO188273
EST:     AATTCTGCACGACCTTTTATCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|33666455|gb|CF297422.1|CF297422
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88848293|gb|CI086815.1|CI086815
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|86432844|gb|CI086455.1|CI086455
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|86414401|gb|CI068804.1|CI068804
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|86880405|gb|CI320946.1|CI320946
EST:     AATTCTGCACGGCCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|396941507|gb|HO188716.1|HO188716
EST:     AATTCTGCACGACCTTTTATCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAAGCTTCTTTATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88277826|gb|CI398628.1|CI398628
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|89196609|gb|CI400779.1|CI400779
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|87028768|gb|CI349487.1|CI349487
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88693826|gb|CI735329.1|CI735329
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|89196661|gb|CI400831.1|CI400831
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|33657910|gb|CF280524.1|CF280524
EST:     AATTTTGCACGACCTTTTACCCTTTTTTCAAAGAGAATCATGATTTTTTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88446710|gb|CI526543.1|CI526543
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88280229|gb|CI401427.1|CI401427
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|9865530|gb|AU101280.1|AU101280
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88996969|gb|CI389635.1|CI389635
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCT-                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88507701|gb|CI435207.1|CI435207
EST:     AATTCTG--CTACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88960061|gb|CI381939.1|CI381939
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|33807485|gb|CF329620.1|CF329620
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88295160|gb|CI525313.1|CI525313
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|86882400|gb|CI325805.1|CI325805
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|157650062|gb|EX449696.1|EX449696
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|58696097|gb|CK084784.1|CK084784
EST:     AATTCTGCACGACCTTTTATCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88508201|gb|CI435707.1|CI435707
EST:     AATTCTG--CTACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88236949|gb|CI236798.1|CI236798
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|66914261|gb|CX101109.1|CX101109
EST:     AAATCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|88491720|gb|CI428992.1|CI428992
EST:     AATTCTG--CTACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
EST: gi|33662437|gb|CF293404.1|CF293404
EST:     AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTG                         GCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA
genomic: AATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAA

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: 70 (upstream exon), 72 (downstream exon)
Score: 64

ATTTATGGAGGTCATTAGTGGAACGGGTGACATAAAAGCTGATATCGAGAAATTCTGCACGACCTTTTACCCTTTTCTCAAAGAGAATCATGATTTTCTGgtatggcctc ... attcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAACAATTACCCACAGAATAAACCTGTCTTACCTGTCTAATGAAATTTAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtctgtaattgtctgattctaatgtgatgtcttccatcatactattcttgcagGCCAGTGTTGGACTTGATGATCTGAAGGCTTCTTAATGCATTCCTATGCAACAATTACCCACAGAATAAACCTGTCTTACCTGTCTAATGAAATTTAGTG
                  ttctaat  putative branch site (score: 64)
                                           ctattctt  putative PPT
                 attctaat  TA-rich tract