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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgtgtttacataatttagtgctcctatcttttgaacagattcattgagtgaaaccaagtattaataatgtttactgttaacaatcggcgatctatttctatttcattaaagatactgatttgccattggacttattatgagatcaaagattgctaatctgcatgtgttattcctgctgtag

Basic information

species Oryza sativa
transcript LOC_Os04g23890.4
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23890.2 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G032351_T01 (Zea mays), 5'ss of exon 15
GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt-gtttacataatttagtgctcctatcttttgaacagattcattgagtgaaaccaagtattaataatgtttactgttaacaatcggcgatctatttctatttcattaaagatactgatttgccattggacttattatgagatcaaagattgctaatctgcatgtgttattcctgctgtag
||||||||||||||||||||||||||| || ||||| || |||||||| ||||  ||| |  |||  ||||||||||  | |||       |     ||| |  | || |      |    ||     ||  |  | | | | |   ||   |  |||||                                                                               
GTTTTATGCTGCAGAGGTTGTAATTGGCCTGGAGTATCTCCATTGCCTTGgtactgatcttatttttataatttagt--ttctagac---aagtgtcttcctcaattgtagt---atgcagattgcagttgttactgagactagaaaatt--tcactatt-------------------------------------------------------------------------------
















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|702138|gb|D48429.1|D48429
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|33799059|gb|CF325389.1|CF325389
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|38470322|gb|CF954453.1|CF954453
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|88306572|gb|CI671324.1|CI671324
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|88580457|gb|CI697388.1|CI697388
EST:     GTTTCATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|29684157|gb|CB680432.1|CB680432
EST:     GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     CTTCATTGCCTAG                         GTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG
genomic: CTTCATTGCCTAGgtatagatgt ... cctgctgtagGTATTATATACCGTGATCTGAAGCCAGAAAACATTTTGCTCCAAGCAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTATGCTGCAGAGGTTGTAATTGGTCTCGAGTACCTTCATTGCCTAGgtatagatgtgtttacataatttagtgctcctatcttttgaacagattcattgagtgaaaccaagtattaataatgtttactgttaacaatcggcgatctatttctatttcattaaagatactgatttgccattggacttattatgagatcaaagattgctaatctgcatgtgttattcctgctgtag

- -  ATGCTG
- - - TGCTGC
- - - - CTGCAG