Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattatattttgttgtcaaacttcattactggaaaaggaaaacgatgccatgggctttttatgctatctatgtatagtgtatgataacactttaagtcttcatgggctttttcaagtgcttccaacatttcttttacacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG

Basic information

species Oryza sativa
transcript LOC_Os11g03730.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 6
gtacattatattttgttgtcaaacttcattactggaaaaggaaaacgatgccatgggctttttatgctatctatgtatagtgtatgataacactttaagtcttcatgggctttttcaagtgcttccaac--atttcttttacacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG
                                               | | | | |       |  | |||| | |  |||||||| |||  ||   | | | ||     ||     | |  ||  | |   ||   | | |||| ||||||||||||||| ||||||||||||||||| ||| | ||||| || |||||||||||||||||||| ||||
-----------------------------------------------aagacctagaaacaa-aaacaatctctttcaagtgtatggtaattctc--actgtgcaaaactttacctgaatatttatagctggttctctctgcacacacagGGACATGGTTTCCGCACAGAACTTATATCCATGCTTTTGGATTTGAAACCACGATTCTTGAGATTTCCTG

upper sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 6
gtacattatattttgttgtcaaacttcattactggaaaaggaaaacgatgccatgggctttttatgctatctatgtatagtgtatgataacactttaagtcttcatgggctttttcaagtgcttc-caacatttctttt----acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG
                                                |||        | |  || |   | |||||||| ||   |       |   | | || ||| |      |||  ||  ||| | | ||| |    | ||| |||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||
------------------------------------------------tgctgaatttatatgttgattcttctgtatagtttactctg-----cttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
















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|29672785|gb|CB669060.1|CB669060
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
EST: gi|29644765|gb|CB649772.1|CB649772
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
EST: gi|29646541|gb|CB651548.1|CB651548
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
EST: gi|29632787|gb|CB637796.1|CB637796
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCA
EST: gi|29638131|gb|CB643140.1|CB643140
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATG
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATG
EST: gi|29680212|gb|CB676487.1|CB676487
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGG
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGG
EST: gi|29674874|gb|CB671149.1|CB671149
EST:     GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAG                         GGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAA
genomic: GAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 70 (downstream exon)
Score: 34

TCAAGGAACAAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAGGGAGTTGTATGGTTTGATCAAGTATCGCTCATGCCTGCAGACACTTACAAGgtacattata ... acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaagtcttcatgggctttttcaagtgcttccaacatttcttttacacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG
                                     tttcttttac  CT-rich tract
                                    atttctttta  TA-rich tract