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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtactccactttttttttattatgaatagaattataaattgtgtatatcattgaaggccttcctgtttgaatgatcataacataattctttatttgcatgtcttcttgtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAATATCACTACTCTTCAAGTTCT

Basic information

species Oryza sativa
transcript LOC_Os04g38480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G870959_T01 (Zea mays), 3'ss of exon 4
gtaagtgtactccactttttttttattatgaatagaattataaattgtgtatatcattgaaggccttcctgtttgaatgatcataacataattctttatttgcatgtcttcttgtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAATATCACTACTCTTCAAGTTCT
               | || | || |||   ||   |||||  ||    |     |||||        || || ||  |||  ||||||  || |||  ||| || ||| |||| ||||| || |||||||| ||||||||||||||||||  |||||| ||| |||||||||||||||  ||||| ||||||||
---------------tcttgtcttgttacttattacattatctataagcttatctattga--------ctattggagggattgtaacatttttatttccttggatatctacttgcaaggacagCCGTCTTAATAACAACAGTCTTTCTGGTCAAATTCCGAAAACCTTGACCAATATCAACACTCTCCAAGTTCT

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtgtactccactttttttttattatgaatagaattataaattgtgtatatcattgaaggccttcctgtttgaatgatcataacataattctttatttgcatgtcttcttgtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAATATCACTACTCTTCAAGTTCT
|| ||| |||         | |   |||       | ||| |   | ||| ||   ||        |  ||||  |||  |       | | |||||  |   |  | | | || ||| |||| || |||||||||||||||||  |||| |||||||| |  ||  |||||||||| ||||| ||||||||  |
gtgagtataca--------tatgctttaccggctcagttacagtctttgtttaatcttagg-----ttttgttccaatttt-------tgactctttgctgaaaattttacatgcaagaatagCCGGCTTAACAACAACAGTCTCACTGGGTCAATTCCTATGTCACTGACCAATATTACTACCCTTCAAGTGTT
















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|44670533|gb|CR283967.1|CR283967
EST:     ACTGGTTTTATTCCGGAAACCTTGGGGCAACTCTACAAGCTGCGTTTCCT                         TCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA
genomic: ACTGGTTTTATTCCGGAAACCTTGGGGCAACTCTACAAGCTGCGTTTCCTgtaagtgtac ... gtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA
EST: gi|29633283|gb|CB638292.1|CB638292
EST:     ACTGGTTTTATTCCGGAAACCTTGGGGCAACTCTACAAGCTGCGTTTCCT                         TCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA
genomic: ACTGGTTTTATTCCGGAAACCTTGGGGCAACTCTACAAGCTGCGTTTCCTgtaagtgtac ... gtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA
EST: gi|58688409|gb|CK077096.1|CK077096
EST:     GCAACTCTACAAGCTGCGTTTCCT                         TCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGANCAA
genomic: GCAACTCTACAAGCTGCGTTTCCTgtaagtgtac ... gtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA
EST: gi|58665168|gb|CK053854.1|CK053854
EST:     ACTGGTTTTATTCCGGAAACCTTGGGGCAACTCTACAAGCTGCGTTTCCT                         TCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA
genomic: ACTGGTTTTATTCCGGAAACCTTGGGGCAACTCTACAAGCTGCGTTTCCTgtaagtgtac ... gtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttgaatgatcataacataattctttatttgcatgtcttcttgtaaggatagTCGTCTTAACAACAACAGTCTTTCTGGTTCAATTCCAAAATCCTTGACCAATATCACTACTCTTCAAGTTCT
            tcataac  putative branch site (score: 2)
                                      tcttcttgt  putative PPT
           atcataacataattct  TA-rich tract