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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggtacttgggttccccttaatttttttcctgttcaacataaactctaataccagtgttggctgtattaatgtttttctgtttttcatcatatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGATGTCTCAACAACAAAAACA

Basic information

species Oryza sativa
transcript LOC_Os02g04660.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G169927_T03 (Zea mays), 3'ss of exon 11
--------ggggtacttgggttccccttaatttttttcctgttcaacataaactctaataccagtgttggctgtattaatgtttttctgtttttcatcatatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGATGTCTCAACAACAAAAACA
          | ||      |||||  | | ||  |   || | |  || || || | |||| ||||| | ||         || | |||||| |||| | ||| ||||||| ||||||| |||||||||| ||||||||||| ||| | |||||||  ||||| ||||| |  || 
tgaacagaatgctatgccttttccctgtgacttcatatttgcttattattaagtccagtacctgtgtttgttg--------attctttgttttacatcttgtgagcagTATCGAAGAGCAGTTGCTAAGGCCTTGGTTGATAGGGTTGCTGATGATGCAGTCTCCACAACTAGGACG

upper sequence: LOC_Os02g04660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G011456_T01 (Zea mays), 3'ss of exon 11
-------ggggtacttgggttcccct-taatttttttcctgttcaacataaactctaataccagtgttggctgtattaatgtttttctgtttttcatcatatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGATGTCTCAACAACAAAAACA
           | |||   || |||| | | ||  |  ||| |||  || || || || ||| ||||| | || ||||       | ||| || |||||| ||  ||||||| ||||||| |||||||||| ||||||||||| ||| | |||||||  ||||| ||||| |  || 
ccagaatcttatcctttcttttccctgtgacttcatgtctgctcattattaagtccaacaccggtgtttgttg-atta-------tttgtattacatcatgtgggcagTATCGAAGAGCAGTTGCTAAGGCCTTGGTTGATAGGGTTGCAGATGATGCAGTCTCCACAACTAGGACG
















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|58682054|gb|CK070741.1|CK070741
EST:     AAGCTCAGACATACGAGACTTTTGAGAAAGATACCGTGAAATATACCCAG                         TATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGAT
genomic: AAGCTCAGACATACGAGACTTTTGAGAAAGATACCGTGAAATATACCCAGgtttctgcta ... atatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGAT
EST: gi|218484593|gb|FG954368.1|FG954368
EST:     AAGCTCAGACATACGAGACTTTTGAGAAAGATACCGTGAAATATACCCAG                         TATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGAT
genomic: AAGCTCAGACATACGAGACTTTTGAGAAAGATACCGTGAAATATACCCAGgtttctgcta ... atatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGAT
EST: gi|58659401|gb|CK048081.1|CK048081
EST:     AAGCTCAGACATACGAGACTTTTGAGAAAGATACCGTGAAATATACCCAG                         TATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGAT
genomic: AAGCTCAGACATACGAGACTTTTGAGAAAGATACCGTGAAATATACCCAGgtttctgcta ... atatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaataccagtgttggctgtattaatgtttttctgtttttcatcatatgaacagTATCAAAGAGCAATTGCTAAGGCATTGGTTGATAGAGTTTCCGATGATGATGTCTCAACAACAAAAACA
                    tattaat  putative branch site (score: 2)
                    tattaatgtttttctg  TA-rich tract