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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttctacatcttacaagcataagacataactgttactacctccgtcccataataattatatttctaggatacaaatttgtcccaaaataattgtca...

Basic information

species Oryza sativa
transcript LOC_Os02g51430.2
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51430.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G070045_T01 (Zea mays), 5'ss of exon 13
GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttctacat-cttacaagcataagacataactgttactacctccgtcccataataattatatttctaggatacaaatttgtcccaaaataattgtca
|||||||||||||| |||||||||||||||||||||||||||||||||||| || ||| | |||||       | | | || ||  ||| ||  | |||| | | | ||  ||| || ||  || ||  ||    || |       
GTTAATTTTGAAGACACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgtgctgcatgcatacaatatagctatacatctatt--tacatc--ttccatgaaagtcat--ttcaagcatttaa-ttgttctttcaacag------

upper sequence: LOC_Os02g51430.2 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA03G03120.1 (Glycine max), 5'ss of exon 19
GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttctacatcttacaagcataagacataactgttactacctccgtcccataataattatatttctaggatacaaatttgtcccaaaata-attgtca-
|||||||||||||||||||| || |||||||||||||| || ||||| ||    |  | |   | |  | |  ||  ||| ||      |  ||    |     || | ||||||    |    ||   | ||| |||   ||    
GTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAGgtatgaaaga-gtgtagaatgttttattcaatacttttctggtgtgtgtgt-gtgtgtgttgtttttctactgcaattgttcagcacaatatatgatgcttt

upper sequence: LOC_Os02g51430.2 (Oryza sativa), 5'ss of exon 17
lower sequence: EFJ12004 (Selaginella moellendorffii), 5'ss of exon 17
GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttctacatcttacaagcataagac-ataactgttactacctccgtcccataataattatatttctaggatacaaatttgtcccaaaataattgtca
|| ||||||||||| ||||| ||||| ||||||||||| ||||||||  |              || || || | || ||       |    |||                                                   
GTCAATTTTGAAGACACCTGTAAAGGGTTTCTTGAGGTGGCCAAGgtgaggagggagatgatgtagaatgaggcgatgacaaagtgcattctcgtag-------------------------------------------------

upper sequence: LOC_Os02g51430.2 (Oryza sativa), 5'ss of exon 17
lower sequence: EFJ08885 (Selaginella moellendorffii), 5'ss of exon 17
GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttctacatcttacaagcataagac-ataactgttactacctccgtcccataataattatatttctaggatacaaatttgtcccaaaataattgtca
|| ||||||||||| || || ||||| ||||||||||| ||||||||  |              || || || | || ||       |    |||                                                   
GTCAATTTTGAAGACACATGTAAAGGGTTTCTTGAGGTGGCCAAGgtgaggagggaggtgatgtagaatgaggcgatgacaaagtgcattctcgtag-------------------------------------------------

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|89171423|gb|CI720482.1|CI720482
EST:     GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAG                         GAGGCAGTCCTTCAAACTGTCAGCGTTATTTTTGAAGACCCAGGTGTACAG
genomic: GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttcta ... atttcaacagGAGGCAGTCCTTCAAACTGTCAGCGTTATTTTTGAAGACCCAGGTGTACAG
EST: gi|88674057|gb|CI728170.1|CI728170
EST:     GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAG                         GAGGCAGTCCTTCAAACTGTCAGCGTTATTTTTGAAGACCCAGGTGTACAG
genomic: GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttcta ... atttcaacagGAGGCAGTCCTTCAAACTGTCAGCGTTATTTTTGAAGACCCAGGTGTACAG
EST: gi|44670727|gb|CR284161.1|CR284161
EST:     GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAG                         GAGGCAGTCCTTCAAACTGTCAGCGTTATTTTTGAAGACCCAGGTGTACAG
genomic: GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttcta ... atttcaacagGAGGCAGTCCTTCAAACTGTCAGCGTTATTTTTGAAGACCCAGGTGTACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAGgtttgttctacatcttacaagcataagacataactgttactacctccgtcccataataattatatttctaggatacaaatttgtcccaaaataattgtca

- - -  TTGAAG
- - - - TGAAGA
- - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccgtccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa