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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattgcctataccttctcttttccttttgactattcaatacttcgatatgcgcattttctagagttttttgtaatacagagcacctttttgctgt...

Basic information

species Oryza sativa
transcript LOC_Os02g03260.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G010044_T02 (Zea mays), 5'ss of exon 9
GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattgcctatacc---ttctcttttccttttgactat----tcaatacttcgatatgcgcattttc-----tagagttttttgtaatacagagcacctttttgctgt
|| ||||||||||| || || || |||||||| ||||||||||| |||||||   ||| | || | |    || || |  ||||| |   ||    |  || | || || |||   |||||     || || | ||||   |||||| ||            
GGTAAGACATCAGTCGATTATGAACCTGTCTACAGTGATGCTCAAGCCAGgtatctataggctgtcctgggttttcatgacctttagctcatgttatgtatgcatctatgtgcatgttttcagttctaaagatatttgctttacagatca------------

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G370852_T03 (Zea mays), 5'ss of exon 10
GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattgcctataccttctctttt---ccttttgactattcaatactt----cgatatgcgcattttc-----tagagttttttgtaatacagagcacctttttgctgt
|| | |||||||||||| ||  | |||||||| ||||||||| ||||||||||| ||| | || | | |  | || |   |||||||   ||   ||   |    | || |||   |||||     || || | ||||   |||||| ||            
GGTAGGACATCAGTTGATTATCAACCTGTCTACAGTGATGCTGAGGCCAGgtgactataggctgtccttgtttttcttgaccttttgctcatgttatgtctgcatctatgtgcatgttttcagttttaaagatatttgccttacagacca------------
















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|2798934|gb|AA752228.1|AA752228
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|88340371|gb|CI659577.1|CI659577
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|29677182|gb|CB673457.1|CB673457
EST:     GCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|218494441|gb|FG968569.1|FG968569
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|58666580|gb|CK055266.1|CK055266
EST:     AAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: AAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|88336267|gb|CI648854.1|CI648854
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|29658442|gb|CB654717.1|CB654717
EST:     CAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: CAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|88307301|gb|CI641939.1|CI641939
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|2312204|gb|C28359.1|C28359
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTTGTTAGTGACTACCGGTTTGATGTATNCCAAATTGGAGCCAGTTATT
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTT-GTTAGTGACTACCGGTTTGATGTAT-CCAAATTGGAGCCAGTTATT
EST: gi|88329810|gb|CI651478.1|CI651478
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|88571723|gb|CI663096.1|CI663096
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|88326072|gb|CI651125.1|CI651125
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|29616438|gb|CB621450.1|CB621450
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|218490400|gb|FG966882.1|FG966882
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC
EST: gi|29628818|gb|CB633829.1|CB633829
EST:     GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAG                         ATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTGTTGC
genomic: GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattg ... tttttttcagATTTGTTAGTGACTACCGGTTTGATGTATCCAAATTGGAGCCAGTTATTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAGACATCAGTTGAATACGAGCCTGTCTATAGTGATGCTCAGGCCAGgtgattattgcctataccttctcttttccttttgactattcaatacttcgatatgcgcattttctagagttttttgtaatacagagcacctttttgctgt

 GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttctct