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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttttctcaatttttttttctagtatgtgtatcagtcttgctaaccaacattatacaatagtagaacttgttttttcctttaaaggaggtgcaattctaagaacattatatagttcaccacaggcatatcgcattactatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG

Basic information

species Oryza sativa
transcript LOC_Os01g25370.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G012601_T01 (Zea mays), 3'ss of exon 7
gtatttttctcaatttttttttctagtatgtgtatcagtcttgctaaccaacattatacaatagtagaacttgttttttcc---tttaaaggaggtgcaattctaagaacattatatagttcaccacaggcatatcgc-attactatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG
||| || ||   || ||| || |||| | |  ||   ||     |      | || | || |    |||    ||         ||  | | |  ||| |  || ||||||||   |||||  ||  | | | | | | ||| | |    |||   | ||||| ||||||||| |          | ||  || |||| ||||| |||||||||||||||||||||||||| || ||||||||||||||||||| ||| | ||||||||||
gtacttctc---atctttgttcctagcaagcatagttgtacctttgtttttccttgtgcagttaatgaatcctttaaaaaaaaattgcacgcaattgccaacctgagaacatt---tagtttgcctaatgtacagcactattcccacttgttcttcagtttgcctaatgtactga----------gtctgtcacttagATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTTGGACAG

upper sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G012601_T02 (Zea mays), 3'ss of exon 7
gtatttttctcaatttttttttctagtatgtgtatcagtcttgctaaccaacattatacaatagtagaacttgttttttcc---tttaaaggaggtgcaattctaagaacattatatagttcaccacaggcatatcgc-attactatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG
||| || ||   || ||| || |||| | |  ||   ||     |      | || | || |    |||    ||         ||  | | |  ||| |  || ||||||||   |||||  ||  | | | | | | ||| | |    |||   | ||||| ||||||||| |          | ||  || |||| ||||| |||||||||||||||||||||||||| || ||||||||||                          
gtacttctc---atctttgttcctagcaagcatagttgtacctttgtttttccttgtgcagttaatgaatcctttaaaaaaaaattgcacgcaattgccaacctgagaacatt---tagtttgcctaatgtacagCACTATTCCCACTTGTTCTTCAGTTTGCCTAATGTACTGA----------GTCTGTCACTTAGATGGGACTGTGGCATGTTCATGCTCAAATACATTGACTTCTACAGCA--------------------------

upper sequence: LOC_Os01g25370.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G088653_T01 (Zea mays), 3'ss of exon 7
gtatttttctcaatttttttttctagtatgtgtatcagtcttgctaaccaacattatacaatagtagaacttgttttttcc----tttaaaggaggtgcaattctaagaacattatatagttcaccacaggcatatcgcattactatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG
||| || ||   || ||| || |||| | |  ||   ||  |  |        || | || |    ||| || |||          |  | | |  ||| |  || ||||||||   |||||    |||| ||      ||| |||    |||  || ||| | ||||||||| | |  |  ||  ||       ||| ||||| || |||||||| |||||||||||||| || ||||||||||||||||||| ||| | ||| ||||||
gtacttctc---atctttgttcctagcaagcatagttgtacttttgtttctgtttgtgcagttaatgaaattctttggaaaaaaactgcatgtaattgccaacctgagaacatt---tagtttcttacag-cac----tattcctacttgttcttaagtttacctaatgtactgagtcttctgtcaccc------tagATGGGACTGCGGCATGTTTATGCTCAAATACATTGACTTCTACAGCAGAGATATGGACCTCATTTTCGGACAG

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|29623085|gb|CB628096.1|CB628096
EST:     CATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGG                         GTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
genomic: CATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttct ... ttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
EST: gi|33692526|gb|CF320765.1|CF320765
EST:     CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGG                         GTGGGAATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAG
genomic: CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttct ... ttccatttagGTGGGA-TTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAG
EST: gi|218485916|gb|FG967011.1|FG967011
EST:     CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGG                         GTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
genomic: CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttct ... ttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
EST: gi|29662159|gb|CB658434.1|CB658434
EST:     CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGG                         GTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
genomic: CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttct ... ttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
EST: gi|29662158|gb|CB658433.1|CB658433
EST:     CTTTCATGGAAGCAGGAGGGTGTAAGAAACCTTCCTTTGCAAGAGAATGG                         GTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
genomic: CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttct ... ttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
EST: gi|58590052|gb|CF988360.1|CF988360
EST:     CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGG                         GTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA
genomic: CTTTCATGGAAGCAGGAGGGTGTAAAAAACCTTCCTTTGCAAGAGAATGGgtatttttct ... ttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatgccttcgaaaatttgcgtaatgtactcattacttggttgccttccatttagGTGGGATTGTGGCATGTTCATGCTCAAATACATAGATTTCTACAGCAGAGATATGGGCCTTACTTTTGGACAG
                                           ccttccattt  CT-rich tract
           aaaattt  TA-rich tract