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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactttctgtccttttcttgcatacaaggaaagctatcatgctttaaccgttccttgccacactgtatttttcagAGGATGCTTATGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCGGAATTTGAG

Basic information

species Oryza sativa
transcript LOC_Os07g22400.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G044317_T04 (Zea mays), 3'ss of exon 4
gtgactttctgtccttttcttgcata-----caaggaaagcta--------tcatgctttaaccgttccttgc--cacactgtatttttcagAGGATGCTTATGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCGGAATTTGAG
||||||| || ||| |||     | |     ||| | ||  ||        | |||||||||| ||| ||||   ||||   | | ||||||||||||||||||| |||||||| | | || || |||||| ||||| |||| || ||||||
gtgacttcctatccatttaccatagaactgacaaaggaaaataatatgcatttatgctttaactgttgcttgttgcacatcatctgtttcagAGGATGCTTATGACTGAGTTTCAATTGCCGTATAAAGCACTGCCATACTCAGAGTTTGAG

upper sequence: LOC_Os07g22400.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G130351_T01 (Zea mays), 3'ss of exon 4
gtgactttctgtccttttcttgcatac------aaggaaagctatc-------atgctttaaccgttccttgccacactgtattt--ttcagAGGATGCTTATGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCGGAATTTGAG
|||| ||||| |   ||| |   | |       ||||||| | ||        |||||||||| ||| ||||   |||   || |  |||||||||||||||||| |||||||| ||| ||||||||||||||||||||||| ||||| |||
gtgattttctataaatttatcatagaactgacaaaggaaaacaatttgtgtttatgctttaactgttgcttgttgcacaacatctgtttcagAGGATGCTTATGACTGAGTTTCAACTGCCATACAAAGCATTGCCACACTCAGAATTCGAG
















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|58665435|gb|CK054121.1|CK054121
EST:     AGACTACGCTTTTTCGCTATCGCTTTCGGCTCGAGAGTCCTGAATCACAG                         AGGATGCTTATGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCG
genomic: AGACTACGCTTTTTCGCTATCGCTTTCGGCTCGAGAGTCCTGAATCACAGgtgactttct ... tatttttcagAGGATGCTTATGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacaaggaaagctatcatgctttaaccgttccttgccacactgtatttttcagAGGATGCTTATGAGTGAGTTTCGACTTCCATACAAAGCATTGCCACACTCGGAATTTGAG
                     ctttaac  putative branch site (score: 3)
                                             tatttttc  putative PPT
                                           tgtattttt  TA-rich tract