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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaacaggacaagtgtacttcctcttaattactataataatcattaattcccaacttgtcctttgcttttgttgatcatatgatgtcgtcctaacaataataatgccaacttgaacag

Basic information

species Oryza sativa
transcript LOC_Os05g51670.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51670.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G038598_T02 (Zea mays), 5'ss of exon 7
GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaacaggacaagtgtacttcctcttaattac-tataataatcattaattcccaacttgtcctttgcttttgttgatcatatgatgtcgtcctaacaataataatgccaacttgaacag
| ||||| ||||||||  |||| |||||||||||||| || ||| |||||||||| || ||||||||||| |||||||| |||||||| | |  |  ||  || ||   |    |  |   | |  |   || || |       ||   ||| ||| |   ||     ||  |||                                
GCTGTGAAGTGTACAACTTGGGGACTGGAAAGGGGACGTCGGTGTTGGAAATGGTGGCTGCATTCGAGAAGGCTTCTGGGAAGgtaaaatcaacgttcacttgaaccatcgtgcatgtgtatgtcttcgccaatattataagggttcgacttggctctgactggctgaattctgtacag----------------------------
















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|218481702|gb|FG969560.1|FG969560
EST:     GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTGGACGAAAGCCTGGAGATGCCGAGATCGTT
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
EST: gi|33681007|gb|CF309246.1|CF309246
EST:     GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
EST: gi|33679559|gb|CF307798.1|CF307798
EST:     GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
EST: gi|33661837|gb|CF292804.1|CF292804
EST:     GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGA-ATGCCGAGATCGTT
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
EST: gi|33686980|gb|CF315219.1|CF315219
EST:     GGACATCTGTGCTGGGAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTG
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTG
EST: gi|218505351|gb|FG968507.1|FG968507
EST:     GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGGCCTGGAGATGCCGAGATCGTT
EST: gi|218498936|gb|FG953341.1|FG953341
EST:     GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAG                         AAAATCCCGCTTGTATTTGCTGGACGAAGG
genomic: GGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaac ... acttgaacagAAAATCCCGCTTGTATTTGCTGGACGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGAGGTGTACAATCTGGGCACTGGAAAGGGGACATCTGTGCTGGAAATGGTTGCAGCATTCGAGAAAGCTTCTGGAAAGgtaaactaacaggacaagtgtacttcctcttaattactataataatcattaattcccaacttgtcctttgcttttgttgatcatatgatgtcgtcctaacaataataatgccaacttgaacag

- - - - - - - - - - - - - - - - - - - - -  GCTGGA