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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagacatcctattctcaattggtttactcctgtttataactactcactagcttacaccaatgttttctgtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCGGCTTAGTAGTGCCATGTTGAGTTTTTGGTTCCAAGTTGGATCAGCAATA

Basic information

species Oryza sativa
transcript LOC_Os02g40880.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G168330_T02 (Zea mays), 3'ss of exon 4
gtcagacatcctattctcaattggtttactcctgtttata---actac-tcactagcttacaccaatgttttctgtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCGGCTTAGTAGTGCCATGTTGAGTTTTTGGTTCCAAGTTGGATCAGCAATA
|||||  | |    | |||| ||  |   |||||||   |   | ||  |  || ||| |||||  | |  | | | | |||||||||| |||||||||||||||||||| || ||||| |||||| |  || |||||||         || ||  |     |||     |||| |      | 
gtcaggaacctccctgtcaaatgtctagttcctgttggcactgagtatattgcttgctcacacctttttcctttatgtaaacagAGGGGTGGTGCTATCAGGCAAGAGCTCGCCAAGCTGAAGAAGGCGTCCACGGCTTAAGTCCCTTTTGGTGGATGGCATGTTAGTTTTTGGTTTCATGTTT

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 4
gtcagacatcctattctcaattggtttactcctgtttataa---ctac-tcactagcttacaccaatgttttct---gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCGGCTTA-GTAGTGCCATGTTGAGTTTTTGGTTCCAAGTTGGATCAGCAATA
|||||  | | |  | |||| ||  |   ||||||| | |    |||  |  || ||| ||||     ||||||    | |||||||||||| |||||||||||||||||||| || ||||| |||||| |  || ||||||| | |||  | |   | |  | |  |   |   |   |  |  || 
gtcaggaaccttcctgtcaaatgtctagttcctgttgacagtgtctatattgctggctcacactttctttttcttttatgtgaacagAGGGGCGGTGCTATCAGGCAAGAGCTCGCCAAGCTGAAGAAGGCGTCCACGGCTTAAGGAGTCTCTTTCCGTGAATGTCATGTTAGAGTTT-TTGGTTATG
















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|89170842|gb|CI040119.1|CI040119
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|427314|gb|D23399.1|D23399
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAG-TCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|88291518|gb|CI537304.1|CI537304
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|8527733|gb|AU092548.1|AU092548
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|88323192|gb|CI550871.1|CI550871
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|88437495|gb|CI528854.1|CI528854
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|86599617|gb|CI253602.1|CI253602
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|88292129|gb|CI534923.1|CI534923
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATNTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTNCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|87011893|gb|CI283780.1|CI283780
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|426714|gb|D22784.1|D22784
EST:     CTTTGACAGGTTCAAGGTTATGTTGNCCAAGATCAAG                         AGGGNAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAANAAGACTGCCGCG
genomic: CTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
EST: gi|55439205|gb|CV732904.1|CV732904
EST:     CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAG                         AGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG
genomic: CGTCACTCAATGACTTTGACAGGTTCAAGGTTATGTTGGCCAAGATCAAGgtcagacatc ... gtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactcctgtttataactactcactagcttacaccaatgttttctgtatgaacagAGGGGAGGTGCTATCAGGCAAGAGCTTGCGAAGCTCAAGAAGACTGCCGCGGCTTAGTAGTGCCATGTTGAGTTTTTGGTTCCAAGTTGGATCAGCAATA
                                       ttttctgt  CT-rich tract
         tttataacta  TA-rich tract