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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaaacagcataaagattttattaggcgggtgaactgcatccatatactgtgccactgatattccttgactgaaatcttcatcccag

Basic information

species Oryza sativa
transcript LOC_Os03g01850.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G143213_T02 (Zea mays), 5'ss of exon 7
GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaaacagcataaagattttattaggcgggtg--------aactgcatc-catatactgtgcca---ctgatattccttgactgaaatcttcatcccag-------------
||| ||||| || || ||||||||| ||||||| ||||| || |  || ||||||| |||| |||||||||||| |||||| || |||||| ||||  |||||||||  ||||   |    |||          || |||||    ||| ||   |||   || | | |   ||  ||  || |  ||||||              
GGTGCTAGGTACACCGAATGAACAAGGTTGGCCTGGAGTCAGTTGTTTGCCTGACTTCAAGACTGCTTTCCCCAGGTGGCAAGCTCAGgtaagaca--acagcataagcatttcgctgcctgggcacctgtggcaagtgcattgtgtatcctcatccatagcttacaatttgtgtttgtcatatgtatcccatgccttcactccag

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G008327_T01 (Zea mays), 5'ss of exon 6
GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaaacagcataaagattttattaggcgggtg----aactgcatc-catatactgtgcca---ctgatattccttgactgaaatcttcatcccag-------------
| ||||||| || || ||||| || |||||||||||||| || |  || ||||||| |||| | |||||||||| |||||| || |||||| | ||  |||||||||  ||||   | |||   ||    || |||||    ||| ||   |||   || | | ||  ||  ||  || |  |||| |              
GATACTAGGTACACCGAATGAGCAGAGTTGGCCAGGAGTCAGTTGTTTGCCTGACTTCAAGACAGCTTTCCCCAGGTGGCAAGCTCAGgtaaggca--acagcataagcatttcgctgggcacatgtggcaagtgcattgtgtatcctcatccatagcttacaatctgtgtttgtcatatatatccgatgcctccattacag
















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|33803869|gb|CF327809.1|CF327809
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88268788|gb|CI378723.1|CI378723
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|3766971|gb|AU031081.1|AU031081
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAANTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|29662032|gb|CB658307.1|CB658307
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88559037|gb|CI489575.1|CI489575
EST:     TTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGNTTTGGACCTTCTC
genomic: TTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88253212|gb|CI351838.1|CI351838
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88978284|gb|CI384727.1|CI384727
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|86885548|gb|CI318699.1|CI318699
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|89196147|gb|CI397149.1|CI397149
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88437700|gb|CI531259.1|CI531259
EST:     TTAGCTCATTACCTGAGTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88488941|gb|CI426212.1|CI426212
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88509819|gb|CI437325.1|CI437325
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88437696|gb|CI531255.1|CI531255
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|38482398|gb|CF966438.1|CF966438
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|66915263|gb|CX102111.1|CX102111
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
EST: gi|88522726|gb|CI450366.1|CI450366
EST:     TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAG                         GCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC
genomic: TTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaa ... ttcatcccagGCTCTTGCAACTATTGTCCCTACTCTTGACCCTGCTGGTTTGGACCTTCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTACTAGGAACTCCAAATGAACAAAGTTGGCCAGGAGTTAGCTCATTACCTGACTACAAGTCTGCTTTCCCCAAGTGGCAGGCACAGgtatgacaaaacagcataaagattttattaggcgggtgaactgcatccatatactgtgccactgatattccttgactgaaatcttcatcccag

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