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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcttctgtttattctgatctgtcatgtatctctaattcctaacatgcttacctccaaggcgaggaggacaaaaagaataaatgtcaacatgtattcctaatattattcatattattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g42260.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 6
gttagtcttctgtttattctgatctgtcatgtatctctaattcctaacatgcttacctccaaggcgaggaggacaaaaagaataaatgtcaacatgtattcctaatattattcatattattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG
|||||||||||   ||  ||| | | || |||   | ||      | |||  |  ||||||            ||    | ||  | || |||   | || || ||  |||||||||||||| ||| |||||||||||||||| |||| | || |||| || ||    ||||| || || ||||||||||| ||||||||||
gttagtcttcttggtaccctggtttatcttgt---tttatcatacatcatagtgtcctcca------------cacttgggattgaagtgaactattgtttcttattgtattcatattattatcagGGTATCAAGACAGAGATTAATCACGTTCTGACTCCCAGAGGTGCAGGCCCAGAAGGGTCATTTATAGGTGTCCAAG
















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|88343088|gb|CI641614.1|CI641614
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCGTGGGCCAGGTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|88342451|gb|CI645973.1|CI645973
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|87006683|gb|CI285717.1|CI285717
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATTCCCATTTTGACACCAAGGTCAGCAGGTCC
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAA-TCCCATTTTGACACCAAGGTCAGCAGGTCC
EST: gi|58608936|gb|CK036969.1|CK036969
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|58676165|gb|CK064852.1|CK064852
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
EST: gi|88290429|gb|CI665218.1|CI665218
EST:     GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAG                         AGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT
genomic: GTCTGCAACAAGTTCAGTCCAGGAGTCCACAGATTCCTGGGCCAGCTCAGgttagtcttc ... ttattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaaaaagaataaatgtcaacatgtattcctaatattattcatattattagcagAGTATCAAGACAGAGATGAATCCCATTTTGACACCAAGGTCAGCAGGTCCTGAGGGGTCATTTATTGGTGTCCAAG
                            tcctaat  putative branch site (score: 2)
                      atgtattcctaatatt  TA-rich tract