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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGT

Basic information

species Oryza sativa
transcript LOC_Os05g37470.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G067022_T02 (Zea mays), 3'ss of exon 4
gtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGT
                                                                                 | |||       |        |   | |||| ||||   | || |     | |  |||   ||| |       | | ||   ||  | || | ||  |   ||||||   ||||| || ||||| ||||| |||||| | |||| ||||||||| ||||||||||||||||||||||| |||||||| |||||  |||||||
--------------------------------------------------------------------------------gtgagccc--ccccggcccccgtcgctcattcaattcatggcggcgtctcgaccagtgttactgact-------gtccctccgcgtgt-cggcgcgccgg-acagGTCCCAGGCGTCACCCACTCTGGCCCCAGCAAGCTCGTGCCCTACTTCACCGGCGCCACCAACATCCTCTACACCTTCGGCGGCCACGCGATCACTGT

upper sequence: LOC_Os05g37470.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 4
gtgagtcctcgatcatcgcccgccgtcgtcggccataaatcaataaatcatcagccggcacatgcttgaccacactgtttataagcatggttgcaatgattatgtatgattcgattcgatggggggctaataacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGT
                                                                               | | ||    |  |    |     ||||  ||   |  | |  |   ||| | ||||    | |  ||||   |    ||| |||   |   ||||  || |  |||  |||   || | |||| | ||  |||||||  ||||||||||||||||||| ||||| ||||| ||||| || || || || || || || |||||
------------------------------------------------------------------------------gtgtgagtggagg-gaggggggcgagtatagtttcgtgagctctgtcacta-tcacgagagctct--ttcgatct--ttgctaatctcttggaactcc-tgccatagGCGGACAATGTCAAGCACACTGGAGCGAGCAAACTGGTGCTCTACTTCACTGGAGCCACAAACATACTCTATACATTTGGAGGCCATGCGGTGACTGT
















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|29638464|gb|CB643473.1|CB643473
EST:     CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAG                         GTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT
genomic: CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctc ... gatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT
EST: gi|86891273|gb|CI307993.1|CI307993
EST:     CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAG                         GTCAACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT
genomic: CCACCTACACCGCCTGGTACCTCGCCATCGCCGCCGCCGTCCACGGCCAGgtgagtcctc ... gatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacgatgtgtatgattcggcgtggccgctgatcgaattcgactcgatgtcgcagGTCGACGGCGTGACGCACTCGGGCCCGAGCAAGATGGTGCTCTACTTCACTGGCGCCACCAACATCCTCTACACTTTCGGCGGACACGCCGTCACTGT
                          cgctgat  putative branch site (score: 4)
          tatgatt  TA-rich tract