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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaaacaacaccagattttttttttttgaaaatttgattgttttgaataccttttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG

Basic information

species Oryza sativa
transcript LOC_Os01g39380.3
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 2
gtgagtcaaacaacaccagattttttttttttgaaaatttgattgttttgaatacct--tttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG
|| ||||||||  || |     ||||    |||| |||| | ||| ||| || || |  |||||||    ||||  |  | || |||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| || |||||||||||| | |||| |  ||  |||||||||||||
gtaagtcaaactgcaac-----ttttgacattgagaatt-ggttgctttaaacacttggtttcttacattttctctacacttcttcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTCCGGATTGGCTATTGGGGGGTTGCTACAGGGAAAAGCCAACCATTGCAGTCATATGGCATGG
















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|58659341|gb|CK048021.1|CK048021
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|701649|gb|D47940.1|D47940
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|87023608|gb|CI286359.1|CI286359
EST:     AGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: AGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|27576987|gb|CA999681.1|CA999681
EST:     GAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: GAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|3763545|gb|AU030297.1|AU030297
EST:     AACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: AACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|163918523|gb|EG713217.1|EG713217
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
EST: gi|163926766|gb|EG715054.1|EG715054
EST:     ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTC                         ATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT
genomic: ATATGATTGAGAAAATAGCTGAGAGAAACAACTTGGGTTACAAGCAGCTCgtgagtcaaa ... ccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaatttgattgttttgaataccttttcttaaccattcttaaaccctcctcagATCAAACTTAGAGCATTGCTCACACATCTGCAACAACTGCGCATTGGCTATTGGGGAGTCGCTACAGGGAAAGGACAACAACCGCCATCATATGGCATGG
                            tcttaac  putative branch site (score: 2)
                                             ccctcctc  putative PPT
              ttttgaata  TA-rich tract