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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGCTGCCCCGGCTGCGCCATGGAGCAGAGGAAGGAGGAGCACAAGGGCATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatatataatatagaattagcacgcatacatgcacagtcaacttagtttgatttgatgtttgtttatctcttcttggtcttatcttattttacttagtacgtagtaacatgcatccttctctgtctctccccttgattttcag

Basic information

species Oryza sativa
transcript LOC_Os11g04030.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04030.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G877788_T03 (Zea mays), 5'ss of exon 1
GATGGCTGCCCCGGCTGCGCCATGGAGCAGAGGAAGGAGGAGCACAAGGGCATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatatataatatagaattagcacgcatacatgcacagtcaacttagtttgatt-tgatgtttgtttatctcttcttggtcttatcttattttacttagtacgtagtaacatgcatccttctctgtctctccccttgattttcag
|| || |||||||||||||||||||| | ||||||||||   | |   ||| | |||||||||||| | || ||||| |||  | ||||| |||| ||| ||| | |  ||       | | ||     | | |   | |   | ||      |||    | ||   |  ||    | ||    ||   | |  | | ||  |                                              
GACGGGTGCCCCGGCTGCGCCATGGACCGGAGGAAGGAGAGCCGCGCCGGCGTCCCCTACAAGGAGCTGCTGTTCGTCGCCGCCGCCACCTTCGCATCCGgtacgtacgtacgtccacgcactactctccgt-ctctcccctccgacaacacctgacgacgctgacggagtagtagtcctcctgctc--cctgctctgctctg----------------------------------------------
















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|29680054|gb|CB676329.1|CB676329
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88359862|gb|CI617773.1|CI617773
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88356270|gb|CI613552.1|CI613552
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|29674310|gb|CB670585.1|CB670585
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|29644401|gb|CB649408.1|CB649408
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCTATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88576396|gb|CI670541.1|CI670541
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|33677870|gb|CF306109.1|CF306109
EST:     CATTCCCTACAAGGAGTTCCTCTTCTTTGTTATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88334950|gb|CI648725.1|CI648725
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88330064|gb|CI652455.1|CI652455
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|33677492|gb|CF305731.1|CF305731
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88347612|gb|CI634297.1|CI634297
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|87008869|gb|CI304812.1|CI304812
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88301079|gb|CI594605.1|CI594605
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCAACACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|29682083|gb|CB678358.1|CB678358
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|29679865|gb|CB676140.1|CB676140
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88332574|gb|CI651734.1|CI651734
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88353644|gb|CI633035.1|CI633035
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|33678908|gb|CF307147.1|CF307147
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88330118|gb|CI650794.1|CI650794
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|29678070|gb|CB674345.1|CB674345
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
EST: gi|88303400|gb|CI669048.1|CI669048
EST:     CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCT                         CTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG
genomic: CATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatat ... tgattttcagCTCTGCCAATCTCTTCCTTGTTCCCCTTCTTGTACTTCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGCTGCCCCGGCTGCGCCATGGAGCAGAGGAAGGAGGAGCACAAGGGCATTCCCTACAAGGAGTTCCTCTTCGTTGCCATCACCACCCTCGCCTCCTgtatgaatatataatatagaattagcacgcatacatgcacagtcaacttagtttgatttgatgtttgtttatctcttcttggtcttatcttattttacttagtacgtagtaacatgcatccttctctgtctctccccttgattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG