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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgcttctgttagcttcttcaattcattcatctcttccttccccattctgaaactgccaagcagtagaaactggagacaaccaacgcacagtcatctgatcagtgcaatcttacatttgccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCAACCAGCCACTGATGAAAGCAGCAATCGCCCTGGACTGTGATTCTGTGAC

Basic information

species Oryza sativa
transcript LOC_Os05g28200.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28200.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G162672_T01 (Zea mays), 3'ss of exon 14
gtgcgcttctgttagcttcttcaattcattcatctcttccttccccattctgaaactgccaagcagtagaaactggagacaaccaac--gcacagtc--atctgatcagtgcaatcttacatttgccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCAACCAGCCACTGATGAAAGCAG---CAATCGCCCTGGACTGTGATTCTGTGAC
                             | || |     ||   ||    |||  ||       |  ||| | ||    ||| |||  ||    ||  |||||||| |  |||| |||| |||||  |    |||||||||| ||||| ||||||||  ||||||| |||||||| || || ||||||||||| | ||||| |||     || |     |  |     |||||    
-----------------------------ttatataagttttggtcaactggaa--tgatttctggatgaatccgggacaaacgaacaggcttcatctgatctgatccggacaattttac-tttgctga---tagGCAAGCGCACAACCATTCTTCGTACTGGGCCTACTGGTGACAGCACTGGCAACCAGCCATTAATGAAGGCAAACTTAAACAGAACGAGCAACCGTTCTGA---
















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|38481364|gb|CF965453.1|CF965453
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|27547699|gb|CA765724.2|CA765724
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88967759|gb|CI098001.1|CI098001
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86540861|gb|CI181067.1|CI181067
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86419098|gb|CI053899.1|CI053899
EST:     TGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86494917|gb|CI137550.1|CI137550
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTTTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88967555|gb|CI014906.1|CI014906
EST:     GTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: GTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|89167777|gb|CI021476.1|CI021476
EST:     GTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: GTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|89176415|gb|CI043436.1|CI043436
EST:     TGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88975033|gb|CI023284.1|CI023284
EST:     AGTTCCGATACTTCCTCAAGGAGCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: AGTTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|88962890|gb|CI025376.1|CI025376
EST:     TGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|86596619|gb|CI286532.1|CI286532
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|3763399|gb|AU030151.1|AU030151
EST:     TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: TTCCAATACTTCCTCAAGGACCCTGTGAAGTATGACGTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
EST: gi|313079556|gb|HO213114.1|HO213114
EST:     GTCAAATACCAG                         GCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA
genomic: GTCAAATACCAGgtgcgcttct ... ccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacaaccaacgcacagtcatctgatcagtgcaatcttacatttgccaaatgcagGCAAGCGCGCAACCGTTCTTCGTCTTGGGCCTTCTGGTGACCGCCCTTGCAACCAGCCACTGATGAAAGCAGCAATCGCCCTGGACTGTGATTCTGTGAC
                                 atcttac  putative branch site (score: 3)
                                    ttacattt  TA-rich tract