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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag

Basic information

species Oryza sativa
transcript LOC_Os03g42220.1
intron # 4
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G058276_T01 (Zea mays), 5'ss of exon 3
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag
|||||||| || |||||| | | ||||||||||||||||||||||||||| ||||||||||| ||||| || ||||| |||||||||||||||||||||||||||||||    | ||| || |   || ||     |  |  |   |   | | ||   |   ||| |   | |      |    | || | |   |   || ||                                                                                      
CAATCAACTGGTAGAGGGCGTAATGTTACTGTTACAAATGATGGGGCTACCATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAAAGGTCCTTGTTGgtatccttt---gtcaatttgattactgttggacgatagtgtttgtaaggtggtaa--taggaatgcaagtgtactttatccccctcccctaaattaattacgtg--------------------------------------------------------------------------------------

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EF517601.1_FGT012 (Zea mays), 5'ss of exon 12
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatccttt--catttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacag-caacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag
|||||||| ||||||||  | | ||||||||||||||||||||||||||| ||||||||||| ||||| || ||||| |||||||||||||||||||||||||||||||  || ||  || |  |||||||| ||      || ||  |   | | || |   | |  ||||||    |   | | | |  | | |  || || |    |                                                                                    
CAATCAACTGGCAGAGGACGTAATGTTACTGTTACAAATGATGGGGCTACCATTTTGAAGTCACTTCACATTGACAATCCTGCTGCAAAGGTCCTTGTTGgtatcctttgccaatttgat-tactgcttgataata----gtattagtaaggtggtaa-taggaaagcaagtgg----gcacctaatgttgtctgtggagtcagccattg------------------------------------------------------------------------------------

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G19220.1 (Glycine max), 5'ss of exon 5
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctt-tcatttgaatctgttgc-ttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag
|| |||||||| |||||  |    |||||||| || |||||||| |||||||| ||||||||||| ||||| || ||||| ||||| || |||||||||||||||||| | ||||     |||||  ||||       | |||     |   | | |  |       |||   || || | | ||      || ||      | | | ||                                                                                   
CAGTCAACAGGTAGAGGACGTGAAGTTACTGTCACTAATGATGGTGCTACAATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttataattttttattgttgtgttgaaagcagcttata-----atttttggagcttg-----gaaagagctaatgtgaaatgcctattcatgttattaaaagggt-----------------------------------------------------------------------------------

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA12G09250.1 (Glycine max), 5'ss of exon 5
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag
|| |||||||| |||||  |    |||||||| || |||||||| |||||||| ||||||||||| ||||| || ||||| ||||| || ||||||||||||||||||  | ||   | | ||| |   || |        || | |   |      || | ||   |   || | | |  | | || ||      |  || | |                                                                                      
CAGTCAACAGGTAGAGGACGTGAAGTTACTGTCACGAATGATGGCGCTACAATCTTGAAGTCCCTCCATATTGATAACCCAGCTGCTAAAGTCCTTGTTGgtatccttgtaatttt-tttattgtt--gtggtgaaagcagcttataatttgttggatcttgga---aagagctatgtgaaatgcttgctcatgctattaataggg-------------------------------------------------------------------------------------

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 5'ss of exon 4
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcc---tttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag
||||| || || |||||       || |||||||| || ||||| ||||| ||| | ||||| ||||| |||||||||||||| || || || |||||||||||     || | |  ||   | | || ||| |  |||||| | |       |   | ||      |    |  ||    |     | |  ||| | |  ||                                                                                           
CAATCTACTGGTAGAGGTCATGCGGTCACTGTTACTAACGATGGTGCTACTATTCTCAAGTCACTTCACATAGACAACCCTGCAGCTAAAGTTCTTGTTGgtatgtaatttccctgcgacattctggcatgaag--ttttcacattcgttttttctta-gttgggttttctctcacagttcgttgtatctggtttgttcttcag------------------------------------------------------------------------------------------

upper sequence: LOC_Os03g42220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv18s0001g00480.t01 (Vitis vinifera), 5'ss of exon 5
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag
|||||||||||||||||  | ||||||||||||||||||||||| ||||| || || |||||||||||||| |||||||| ||||| || |||||||||||||||||| |  | |   ||||   |   |||| || |    |      || |    | |||    |  |||  | ||   || |||  || | ||  || |   |                                                                                     
CAATCAACAGGCAGAGGCCGCAGTGTTACTGTTACAAATGATGGTGCTACCATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttactatagttgctgtca-tcattgatgttgctgttttggttcat-gtggattataacatatatggtcatgga--aaattt--ttgaaactccaccgcac-------------------------------------------------------------------------------------

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|58684862|gb|CK073549.1|CK073549
EST:     AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTG                         ACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
genomic: AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttc ... gcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
EST: gi|29676853|gb|CB673128.1|CB673128
EST:     AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTG                         ACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
genomic: AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttc ... gcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
EST: gi|29657046|gb|CB653321.1|CB653321
EST:     AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTG                         ACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
genomic: AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttc ... gcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
EST: gi|29616345|gb|CB621357.1|CB621357
EST:     AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTG                         ACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
genomic: AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttc ... gcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
EST: gi|88422879|gb|CI615179.1|CI615179
EST:     AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTG                         ACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG
genomic: AATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttc ... gcattgttagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCAACAGGCAGAGGGAGGAGTGTTACTGTTACAAATGATGGGGCTACAATTTTGAAGTCCCTTCATATAGACAACCCTGCTGCAAAGGTCCTTGTTGgtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG