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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT

Basic information

species Oryza sativa
transcript LOC_Os04g55940.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
|||||| | ||| | | ||||  | |||  | | |  |||   ||  |  || ||    |  || |   |  |||         | ||||||||| || ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || ||| |
gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcct--caaatggtgacttactg----aactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCATTGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
gtatgcatttttatttttatgatttataacctattacaaa--atggagaaccagtgaac---aataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
|||||| | ||| | ||||||  | ||| || |||  |||  ||     |  || |  |   |||  |      ||||   |       | ||||||||| || ||||| |||||||| || ||||||||||| ||||||||||| ||| |||||||||||||||||||||||||||||||||| || || ||| |
gtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgatttcaactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCATTGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
             | |   |  |||||  ||  ||      |  |   || ||   |  |     ||  |  ||  |  | |    |||||||||||| || || ||||| || || || ||||||||||||||||| ||| |||| ||||| |||||||     |||||  | || ||||| |||||  |
------------gtatccctcttttatttccctttttctctt--aaggcccgtatcctcttttcaac--tcactcgtgttgctttctgcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagac--attttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
|||| |   ||||||||  |  | | |  |   |||  |            ||   |     ||     | |  ||| |  |     ||||||||||||| || || ||||| || ||||| ||||||||||||||||| ||| |||| ||||| ||| |||     |||||  | || ||||| ||||| ||
gtatcctcatttattttctttttcttttcctatttatcattctctccctttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT

upper sequence: LOC_Os04g55940.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
-----gtatgcatttttatttttatgatttataacctattacaaaatggagaaccagtgaacaataacagacattttcttttaatacc---gat-tgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
       |    ||| |||| ||    | | || ||| |     |   |    | | |      |        |||  ||||  | ||   ||| |||||||||||| |||||||||||||| || || ||||| || |||||||| ||  |||| ||||| |||||  |||| |||||  |||| ||||| ||||||||
ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT

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|88763180|gb|CI772736.1|CI772736
EST:     GCAGCTCGCAATATACACTGGTCCAACAG                         TTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAG
genomic: GCAGCTCGCAATATACACTGGTCCAACAGgtatgcattt ... ccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaatggagaaccagtgaacaataacagacattttcttttaataccgattgcagTTGGGGGGCTTCTAAATGCTACGTTCGGAAATGCAACTGAAATGATCATAGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTTCAACAATCATT
                             acattttcttttaata  TA-rich tract