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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctcatacatttgttatgtgcattgtgctatttcttattggtaccatcttaacacttctttcccttttgttttcattgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag

Basic information

species Oryza sativa
transcript LOC_Os11g24540.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G082330_T01 (Zea mays), 5'ss of exon 6
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctcatacatttgttatgtgcattgtgctatttcttattggtac-catcttaacacttctttcccttttgttttca--ttgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag
|||| |||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||| ||||||||||| ||||||||||||||||||||||||||||  ||| |   |  |  |     ||| | |||| |  || | || |  ||    |    | |||||||||||||      || |    ||| ||  |   |  | || | || ||                                                  
TATTATAGTAGCTTCAGTTTTCCTCCTCCTCCTGTTCTACTTCATGTCATCTTGGTTCGTTTGGGTGCTAATTGTACTATTCTGCATTGGTGGTATTGAGgtattccctcctt--tcgggcacagtaattcttctatcttgtactagtgcatattgatatgtatttttcccttttgttggggagttcagcactgaggttaatggtgatattatcttgcag-------------------------------------------------

upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G082330_T03 (Zea mays), 5'ss of exon 6
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctcatacatttgttatgtgcattgtgctatttcttattggtac-catcttaacacttctttcccttttgttttca--ttgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag
|||| |||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||| ||||||||||| ||||||||||||||||||||||||||||  ||| |   |  |  |     ||| | |||| |  || | || |  ||    |    | |||||||||||||      || |    ||| ||  |                                                                    
TATTATAGTAGCTTCAGTTTTCCTCCTCCTCCTGTTCTACTTCATGTCATCTTGGTTCGTTTGGGTGCTAATTGTACTATTCTGCATTGGTGGTATTGAGgtattccctcctt--tcgggcacagtaattcttctatcttgtactagtgcatattgatatgtatttttcccttttgttggggagttcagcactgaggttaat-------------------------------------------------------------------

upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA08G47600.1 (Glycine max), 5'ss of exon 5
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtatttt--ctcatacatttgttatgtgcattgtgctatttcttattggtaccatcttaacacttctttcccttttgttttcattgaatgt-tgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag
| |  ||| ||| ||    || ||  | ||  | |||| ||| ||||| |||||||| |||||| |||| |||||| | |||||||||||||||||||||||| | |  |||||    |||  || || | | | ||  | ||        || ||| |  |          |  | ||| ||| |  ||  |||||                                                                        
TGTCATAGCAGCGTCTACCTTTCTTGTGCTATTGTTCTTCTTTATGTCATCTTGGTTTGTCTGGGTGCTGATTGTACTTTTCTGCATTGGTGGTATTGAGgtaatgtagctcatttccttgg-atttggaatttacttctactctagtactccttctaattaacaaaaaaaatcatattt-catggtgtgcatgaagggggt-------------------------------------------------------------------

upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G44490.1 (Glycine max), 5'ss of exon 6
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctcatacatttgttatgtgcattgtgctatttcttattggtaccatcttaacacttctttcccttttgttttcattgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag
  |  |    || ||   ||| ||  | || || |||| ||||||||| ||||||||  ||||| |||| ||| || | |||||||||||||||||||||||    |  |  |  || ||    |    |       |||  |||   || |     | |  |  || | |  |||   ||   | |||||       |||| || ||                                                          
CGTCATCACTGCATCTACTTTTCTTGTACTACTGTTCTTCTTCATGTCGTCTTGGTTTATCTGGGTGCTGATTATACTTTTCTGCATTGGTGGTATTGAGgtgaggtagctcattttcgtggattttgctcctaaccttccaattaaaacaaat---atatcttatttcatgatgtgccca--aagtgttg----gctccttattcttg---------------------------------------------------------

upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G39260.1 (Glycine max), 5'ss of exon 5
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctcatacatttgttatgtgcattgtgctatttcttattggtaccatcttaacacttctttcccttttgttttcattgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag
  |  |    || ||   ||| ||  | || || |||| ||||||||| ||||||||  ||||| |||| ||| || | |||||||||||||||||||||||         ||||||| |  ||    ||   |     ||| |   ||  ||    | |  |  || | |  |||   ||     ||| |     | |||| || || ||                                                       
CGTCATTACGGCATCTACTTTTCTTGTGCTACTGTTCTTCTTCATGTCGTCTTGGTTTATCTGGGTGCTGATTATACTTTTCTGCATTGGTGGTATTGAGgtgag-----gtacattt-tcgtggattttactcctaaccttctaattaaaataactatatcttatttcatgatgtgccca--aggtgtcg----gttccttattcttgttc------------------------------------------------------

upper sequence: LOC_Os11g24540.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G53880.1 (Glycine max), 5'ss of exon 5
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtatttt--ctcatacatttgttatgtgcattgtgctatttcttattggtaccatcttaacacttctttcccttttgttttcattgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag
| |  ||| ||| ||    || ||  | ||  | |||| |||||||||  ||||||| |||||| |||| |||||| | |||||||||||||||||||||||| | |  |||||    |||  || || | | | ||  | ||   ||||||  | |  |     ||     |  ||||| ||| |  ||    |       ||                                                                
TGTCATAGCAGCGTCTACCTTTCTTGTGCTATTGTTCTTCTTCATGTCAACTTGGTTTGTCTGGGTGCTGATTGTACTTTTCTGCATTGGTGGTATTGAGgtaatgtagctcatttccttgg-atttgaaatttacttctact--ctggtactctttctaattaactaaatatcatgttt-catggtgtgcatgaaggggtatt----------------------------------------------------------------

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|29667215|gb|CB663490.1|CB663490
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|58601056|gb|CK011584.1|CK011584
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|218487041|gb|FG950201.1|FG950201
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTGGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88688575|gb|CI732151.1|CI732151
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88688415|gb|CI731991.1|CI731991
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTNTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|286796|gb|D15603.1|D15603
EST:     GTCTGGCCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: GTCTGG-CTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88691769|gb|CI733346.1|CI733346
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88691004|gb|CI735083.1|CI735083
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|218478582|gb|FG949084.1|FG949084
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88690551|gb|CI734630.1|CI734630
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|396941284|gb|HO188493.1|HO188493
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88688359|gb|CI731935.1|CI731935
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|88691243|gb|CI733827.1|CI733827
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTNTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|58592179|gb|CF990487.1|CF990487
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|218504564|gb|FG954781.1|FG954781
EST:     CTAATTGTA-TATTCTGCATTGGTGGTATTGAG                         GGTATGCATG-TTGCTTGGTCACACTTCTCACTAG
genomic: CTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG
EST: gi|29664758|gb|CB661033.1|CB661033
EST:     CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAG                         GGTATGCATGTTTGCTTGGTCACACTTCTCACTAN
genomic: CTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctc ... aattttacagGGTATGCATGTTTGCTTGGTCACACTTCTCACTAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTTTAGTAGCTTCAGTTTTCCTCCTCCTCCTCTTCTACTTCATGTCTTCTTGGTTCGTCTGGCTGCTAATTGTATTATTCTGCATTGGTGGTATTGAGgtattttctcatacatttgttatgtgcattgtgctatttcttattggtaccatcttaacacttctttcccttttgttttcattgaatgttgaagtataccttttttttttttttcattttcctttgttgagagattcagctatgagactgactatgaattttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG