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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggtttatgtttgtggtgtttttcattcagttgcatcactacattttatgcagagtcattaacaaagagatgtttatgcatataccttttcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTATTTGACTATGTATTGCATCAAATAAATGAAACATTCTTGGCTGGCGGCC

Basic information

species Oryza sativa
transcript LOC_Os01g74310.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G459642_T02 (Zea mays), 3'ss of exon 3
----gaggtttatgtttgtggtgtttttcattcagttgcatc------actacattttatgcagagtcattaacaaagagatgtttatgcatataccttttcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTATTTGACTATGTATTGCATCAAATAAATGAAACATTCTTGGCTGGCGGCC
      |  |||   | | ||| || ||  || || ||| |        | |  ||||||    ||| | | |     | |||||| |  || || |      ||| |||||||||||||||||||||||||| |||||||||||||||||||||||  | |||||||| ||| ||||||||||||||||  ||| ||||||||| ||  
aattccgacttacactggaggt-ttcttggttaagatgctttccatttgccatcttttatatgtagttagtga-----aaatgttttt-tatctatcacc---tttacagTATTCACGAGCCAACTCAAGGGAAGAGAAGCGGGATTTGTTCTTTGTCATTTTTGACTACGTAGTGCATCAAATAAATGAGGCATGCTTGGCTGGTGGTA

upper sequence: LOC_Os01g74310.5 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0019g00680.t01 (Vitis vinifera), 3'ss of exon 11
gaggtttatgtt-tgtggtgtttttcattcagttgcatcactacattttatgcagagtcatt--aacaaagagatgtttatgcatataccttttcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTATTTGACTATGTATTGCATCAAATAAATGAAACATTCTTGGCTGGCGGCC
     ||||||  |  |  |      ||| | ||  || |||| |  ||||  | |   |||   ||    | ||| | |    |      ||||| | |||||| || |  |||||||||||||| ||||   |  || | |   | || || ||||||||||| ||||||||||| |||||||||| | | |||  | |  
-gttgttatgtcataagcagaagcggatttatttctat-actaaaacttatttaaatctattttgacctttacatgataacttcttagttctttcaat-gcagTACTCGCTTGCCAACTCAAGGGAAGAGAGAAGAAATCTATATCTGGTGCTTTTTGACTATGTTTTGCATCAAATTAATGAAACATGCATAGCTACCAGTG
















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|29640366|gb|CB645375.1|CB645375
EST:     TTCCTGACCAGATAGATCGCGTTGGTGGAGTTGACTATATCTGTCTCGAG                         TATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTA
genomic: TTCCTGACCAGATAGATCGCGTTGGTGGAGTTGACTATATCTGTCTCGAGgttagtttta ... tcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTA
EST: gi|88395645|gb|CI590660.1|CI590660
EST:     TTCCTGACCAGATAGATCGCGTTGGTGGAGTTGACTATATCTGTCTCGAG                         TATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTA
genomic: TTCCTGACCAGATAGATCGCGTTGGTGGAGTTGACTATATCTGTCTCGAGgttagtttta ... tcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTA
EST: gi|29675980|gb|CB672255.1|CB672255
EST:     GTTGACTATATCTGCCTCTAG                         TATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTA
genomic: GTTGACTATATCTGTCTCGAGgttagtttta ... tcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgcagagtcattaacaaagagatgtttatgcatataccttttcatttgcagTATTCACGAGCCAACTCAAGGGAGGAGAAGCGGGATTTGTTCTTTGTTCTATTTGACTATGTATTGCATCAAATAAATGAAACATTCTTGGCTGGCGGCC
            cattaac  putative branch site (score: 2)
                                        ccttttcattt  putative PPT
             attaacaaa  TA-rich tract