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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgtgtgctatgtagcattttcgttactggtactttatggatcttttgaactcatctcatatcatttcctttgctttgatctgcttttgttccgacattccttaaaactgctggggtgttgatattcaag

Basic information

species Oryza sativa
transcript LOC_Os10g32730.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32730.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G027115_T01 (Zea mays), 5'ss of exon 6
GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgtgtgctatgtagcattttcgttactggtactttatggatcttttgaactcatctcatatcatttcctttgctttgatctgcttttgttccgacattccttaaaactgctggggtgttgatattcaag
| ||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||  |||||||||      ||||   |        | |  |     |   || |||   |  | |||||   || | |||||   |   ||||| || |  |||||                                      
GGTGGAAAGAGTCTTTCTCTGCAATTGTTGGTGGAGATGAAGTAGAGAAGGGGAAGCCATCCCCGAATATgtaagatatcatgctgcatgatgccaccatctcatactccagattgattaatgcatctcatt--atcttatttctgatatgttgatgtgatggtgttcaag-----------------------------------
















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|157651850|gb|EX451484.1|EX451484
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGGAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|29687643|gb|CB683918.1|CB683918
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|29671819|gb|CB668094.1|CB668094
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|29658982|gb|CB655257.1|CB655257
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|29629324|gb|CB634335.1|CB634335
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|58688816|gb|CK077503.1|CK077503
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGC
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGC
EST: gi|29679504|gb|CB675779.1|CB675779
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|29623338|gb|CB628349.1|CB628349
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
EST: gi|29659012|gb|CB655287.1|CB655287
EST:     GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATAT                         ATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT
genomic: GCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgt ... gatattcaagATTTTTGGAAGCTGCAAAACGAATGAATACAAATCCTCCAAATTGCTTAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGAAAGAGTCGTTCTCCGCAATTGTTGGTGGTGATGAAGTAGAGAAGGGGAAGCCATCCCCAGATATgtaaggctgtgtgctatgtagcattttcgttactggtactttatggatcttttgaactcatctcatatcatttcctttgctttgatctgcttttgttccgacattccttaaaactgctggggtgttgatattcaag

- - - - - - - - - - - - - - TGGTGG