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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaacttatgtgcaccttgaggctagctagctgtcatatctgcagggaggttttgtccatgaatatataattcttgatatggttccttcactcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTGTTGGATTCCTCGATCCCAATGAGTAGATGCGCCATTGAGCCTGAGGCCA

Basic information

species Oryza sativa
transcript LOC_Os07g12830.1
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g12830.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G152438_T02 (Zea mays), 3'ss of exon 6
-gaac-ttatgtgcaccttgaggctagctagctgtcatatctgcagggaggtt--ttgtccatgaatatataattcttgatatggttccttcactcccctat-agACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTGTTGGATTCCTCGATCCCAATGAGTAGATGCGCCATTGAGCCTGAGGCCA----
 || |  ||||    | |||  |||   | |||   || ||| |  |   |||  |||| |||     |||||||||||||   | ||||| |||   |||| ||| ||||| ||||| |||||||||   || ||||||||||||||||||||||| |||||||| |||||||  | ||||||   |      | || | | ||    
cgatcactatgatgcctttgcagct--tttgct-caatctcttcgtgattgttgattgtgcatctgcttataattcttgatt--gctccttgacttgactattagATAAATACCATGCTTGGGTAAATGCAGAGTTCCTCCTGGAGAAGTGCCTTGTCGGATTCCTTGATCCCACCGCGTAGATATCC----AGGTCTCATGGCATTTT

upper sequence: LOC_Os07g12830.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G167946_T01 (Zea mays), 3'ss of exon 2
----gaacttatgtgc--accttgaggctagctagctgtcatatc-tgcagggaggttttgtccatgaatatataattcttgatatggttccttcactcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTGTTGGATTCCTCGATCCCAATGAGTAGATGCGCCATTGAGCCTGAGGCCA
      | | |  | |  |   | |   | | |  || ||  ||  ||  |       | || |||     |||||||||||||   | ||||| |||   |||| || ||||| ||||| |||||||||   || |||||| |||||||||||||||| |||| ||| ||| |||| | ||||||  |     | | || ||||| 
ttggtgattgacctactgatgattacatttgtttactatcccattatgtggttgtagatcgtgcatctgcttataattcttgatt--gctccttgacttgacTATGGATAAATACCATGCTTGGGTAAATGCAGACTTCCTCTTGGAGAAGTGCCTTGTCGGATCCCTTGATTCCAAAGCGTAGATATG-----GGGGCTCAGGCCG
















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|86252073|gb|CI055810.1|CI055810
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
EST: gi|33680256|gb|CF308495.1|CF308495
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
EST: gi|88491319|gb|CI428591.1|CI428591
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
EST: gi|86420762|gb|CI056751.1|CI056751
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
EST: gi|3762892|gb|AU029644.1|AU029644
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCCTGGAGAAGTGCCTT
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCT-CCTGGAGAAGTGCCTT
EST: gi|88990983|gb|CI108370.1|CI108370
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
EST: gi|88831337|gb|CI082147.1|CI082147
EST:     AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCA                         ACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG
genomic: AGTTGATATGCTTATGAAGGCTGCTGGAAAAGACTCGACCGCTCTGTTCAgtatccttct ... tcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggttttgtccatgaatatataattcttgatatggttccttcactcccctatagACAAATATCATGCATGGGTAAATTTTGAATTCCTCCTGGAGAAGTGCCTTGTTGGATTCCTCGATCCCAATGAGTAGATGCGCCATTGAGCCTGAGGCCA
                                    ttccttcac  putative branch site 
                                    ttccttcactccccta  CT-rich tract
            atgaatatataattct  TA-rich tract