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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatccactgtactctacagtattcatcatcaaataatgctcttcatgtcaaatgagtctgatccttaattaacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g39380.1
intron # 29
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 29
lower sequence: GRMZM2G074466_T01 (Zea mays), 3'ss of exon 9
gtatgtgaccattgcttattttaaaactggggagatgagctctatcacatatccactgtactctacagtattcatcatcaaataatgctcttcatgtcaaatgagtctgatccttaattaacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
||||||||| ||  || ||||||| |   ||| |                     ||| | | |   | ||  ||  |  ||||    ||| ||||         |||||| |||||||   || ||||||||  |||||||||| ||||| ||||||||||||||||
gtatgtgactatatctcattttaagaacagggtggc-------------------ctgaattgt---ggatctatagttgaata---ttctgcatgct-------tctgattcttaatt--tattccagGTTCAGCTGATGGGCTCATACGATTTTGGGAAAATGAAG
















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|86504094|gb|CI146727.1|CI146727
EST:     CTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|29628945|gb|CB633956.1|CB633956
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|29641895|gb|CB646902.1|CB646902
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|29639658|gb|CB644667.1|CB644667
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|66923642|gb|CX110490.1|CX110490
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAA
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAA
EST: gi|58694575|gb|CK083262.1|CK083262
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|27547319|gb|CA765549.2|CA765549
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|22304904|gb|BQ906126.1|BQ906126
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|325493716|gb|JG458240.1|JG458240
EST:     CCCAATACTCTGTGTTGAGTACTCAACCTCAGATAACGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTATGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
EST: gi|38476896|gb|CF961029.1|CF961029
EST:     CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGG                         GTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
genomic: CCCAATACTCTGTGTTGAGTACTCACCCTCAGATAAAGGAATCATCACGGgtatgtgacc ... aacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcaaataatgctcttcatgtcaaatgagtctgatccttaattaacatcccagGTTCCTCTGATGGGCTTATACGTTTTTGGGAAAATGAAG
                                         aattaac  putative branch site (score: 2)
                                       ttaattaacat  TA-rich tract