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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTAAAGAGTGTCCTCTTCCTTATGCCTTGCCATTCAACACCTTATTACTCTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgccttcacttttttctagtgcagtagatatagcatttcattttactatgttgtacctgatttagccaattatcctgacttagcgtgcttgttaccag

Basic information

species Oryza sativa
transcript LOC_Os02g02110.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02110.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G000937_T02 (Zea mays), 5'ss of exon 9
GAGTAAAGAGTGTCCTCTTCCTTATGCCTTGCCATTCAACACCTTATTACTCTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgccttcacttttttctagtgcagtagata--tagcatttcattttactatgttgtacctgatt-tagccaattatcctgacttagcgtgcttgttaccag
|||| | |||||| ||||| || |||||||| |||||||||||||| ||||| || ||||||||||| || |||||||| ||||||||||| ||||||||||| |||| || | |||| || || | | ||| || | |||||| | || |||| | ||| | | | |||||| | || | |||
GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttat--tttatttgttttttaatgaaaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatatgtccctgctgactcgttctact-gcactcag

upper sequence: LOC_Os02g02110.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G164175_T02 (Zea mays), 5'ss of exon 9
GAGTAAAGAGTGTCCTCTTCCTTATGCCTTGCCATTCAACACCTTATTACTCTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgccttcacttttttctagtgcagtagata--tagcatttcattttactatgttgtacctgatt-tagccaattatcctgacttagcgtgcttgttaccag
|||| | |||||| ||||| || |||||||| |||||||||||||| ||||| || ||||||||||| || |||||||| ||||||||||| ||||||||||| |||| ||| | |||| || || | ||| || | |||||| | || |||| | ||| | | | | ||||| | || | |||
GAGTGAGGAGTGTTCTCTTTCTCATGCCTTGTCATTCAACACCTTACTACTCAACCTTACATTACAATCTACCTATGCGTTTTTTGGACTGCACTCCTAGgtggttat--tttctttgttttttaatgacaaaaatagttaacctttcatatctatac-ttgtgcttgaatacatacgtccctgctgacgcgttctact-gcactcag
















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|86484223|gb|CI126856.1|CI126856
EST:     TCTACAGTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAG                         CGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT
genomic: TCTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgc ... ttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT
EST: gi|88522669|gb|CI449426.1|CI449426
EST:     ATTACAACCTGCCTATGCGCTTTTTGGGACTGTACTCCTAG                         CGAAAAACAAAGGGACCTTGGATGAGTCAGATCNTTTCCTCATGAACCCAT
genomic: ATTACAACCTGCCTATGCGCTTTTT-GGACTGTACTCCTAGgtgattatgc ... ttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT
EST: gi|88525233|gb|CI454218.1|CI454218
EST:     ACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAG                         CGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT
genomic: ACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgc ... ttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT
EST: gi|88524824|gb|CI453773.1|CI453773
EST:     TTTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAG                         CGAAAAACAAAGGGACCCTTGGATGAGTCAGATCGTTTCCTCATGAACCCA
genomic: TCTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgc ... ttgttaccagCGAAAAACAAAGGGA-CCTTGGATGAGTCAGATCGTTTCCTCATGAACCCA
EST: gi|88557403|gb|CI487804.1|CI487804
EST:     ACCTGCCTATTGCGCTTTTTGGACTGTACTCCTAG                         CGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT
genomic: ACCTGCCTA-TGCGCTTTTTGGACTGTACTCCTAGgtgattatgc ... ttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCAT

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: 49 (upstream exon), 56 (downstream exon)
Score: 10

GAGTAAAGAGTGTCCTCTTCCTTATGCCTTGCCATTCAACACCTTATTACTCTACATTACATTACAACCTGCCTATGCGCTTTTTGGACTGTACTCCTAGgtgattatgc ... ttgttaccagCGAAAAACAAAGGGACCTTGGATGAGTCAGATCGTTTCCTCATGAACCCATCAGATTTTGTGGGCAAGGTTTTTGGAAATTTATCTTCTTTCAGTCACAT




<











<


<