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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCCTTTCCAGCTAGGGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaacagagaattgcttcatgattttgatgtactcaagtgcttttctagtttctgccaagcaaatcataaataacaggatttgggcctgtccat...

Basic information

species Oryza sativa
transcript LOC_Os03g42750.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G099056_T01 (Zea mays), 5'ss of exon 23
ATTCCTTTCCAGCTAGGGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaacagagaattgcttcatgattttgatgtactcaagtgcttttctagtttctgccaagcaaatcataaataacaggatttgggcctgtccat--
|| || || ||||| ||  | ||||||||||| |||||||||||  | |||||||| ||||||||||||||| |||   | |  |||||||||| |  | ||||||  || ||||||        ||    |||  |  | | |    |   |  |   || ||    
ATACCGTTTCAGCTGGGATTATCAAAAACTGACCTAAGGAGGGTACTGAAATCCAGCTTATCTGGGgtaagt-aaatctatatctgcttcatgaatcagttgtacttcagagctttttacagagttgggtggcag-ttgtcacttcttgccctaagctgtgacctgtg

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA14G08570.1 (Glycine max), 5'ss of exon 4
ATTCCTTTCCAGCTAGGGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaacagagaattgcttcatgattttgatgtactcaagtgcttttctagtttctgccaagcaaatcataaataacaggatttgggcctgtccat
|||||||| ||||| || ||||||||||  |||||  ||| | || | ||||||||||||||||||||| |   |        ||  || | |||  |  |  |||   ||  | | |  | || ||  |   |  || |   |       || |           
ATTCCTTTTCAGCTTGGACTGTCAAAAATGGATCTTCGGAAGATGTTAAAATCCAGTTTATCTGGGgtatggtgattctgatcttctttaaagatccttct-cact---gttgtatgcctgcttttga-acttatgtctttgctcttctacttag-----------

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA17G36540.1 (Glycine max), 5'ss of exon 23
ATTCCTTTCCAGCTAGGGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaacagagaattgcttcatgattttgatgtactcaagtgcttttctagtttctgccaagcaaatcataaataacaggatttgggcctgtccat
|||||||| ||||| || ||||||||||  |||||  ||| | || | ||||||||||||||||||||| |   |        ||  || | |||  |  |  |||   ||  | | |  |  | ||  |   |  || |   |       || |           
ATTCCTTTTCAGCTTGGACTGTCAAAAATGGATCTTCGGAAGATGTTAAAATCCAGTTTATCTGGGgtatggtgattctgatcttctttaaagatccttct-cact---gttgtatgcctgcctttga-acttatgtctttgctcttctacttag-----------

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 5'ss of exon 23
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 5'ss of exon 23
ATTCCTTTCCAGCTAGGGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaacagagaattgcttcatgattttgatgtactcaagtgcttttctagtttctgccaagcaaatcataaataacaggatttgggcctgtccat
|| ||||||||||| ||  |||||||||  |||||  ||| | || | ||||||||||||||||||||||||||          | |||  |    |   ||||  |   | |||    | |  |||   |    |||||   |  ||   |   |          
ATCCCTTTCCAGCTGGGATTGTCAAAAATGGATCTTCGGAAGATGTTGAAATCCAGTTTATCTGGGgtaagtcagttga-----tactttctagagtccctgtatgcctattcttagacaatcactgtttaaactatcatgtgttccattgtacag----------

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|29667112|gb|CB663387.1|CB663387
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|29656592|gb|CB652867.1|CB652867
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|29657699|gb|CB653974.1|CB653974
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|58680504|gb|CK069191.1|CK069191
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAAT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAAT
EST: gi|29639555|gb|CB644564.1|CB644564
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|38477138|gb|CF961271.1|CF961271
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|29676302|gb|CB672577.1|CB672577
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|29645304|gb|CB650311.1|CB650311
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
EST: gi|29627167|gb|CB632178.1|CB632178
EST:     GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGG                         ATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT
genomic: GGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaa ... acatgtgcagATTGACAAGTCAATCGGTGCCATGTATAGGAGGTTACAGAAGACACTGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCCTTTCCAGCTAGGGCTGTCAAAAACTGATCTAAGGAGGGTGATCAAATCCAGTTTATCTGGGgtaagtcaaacagagaattgcttcatgattttgatgtactcaagtgcttttctagtttctgccaagcaaatcataaataacaggatttgggcctgtccat

- - - - - - - - - - - - - - - - -  AAGGAG