Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACGCTGCTGCTCTCCCGCGGCGAGCTCCGCGTCCACGTCCTCGGCTGGATCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagcaaacgaatgcaatcttgatgtcttgctaactaatcgctcgatcgatcaaccagcagctgatgacaaggttctgatgattgttgtgttttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g30910.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g30910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G872392_T02 (Zea mays), 5'ss of exon 4
CACGCTGCTGCTCTCCCGCGGCGAGCTCCGCGTCCACGTCCTCGGCTGGATCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagcaaacgaatgcaatcttgatgtcttgctaactaatcgctcgatcgatcaaccagcagctgatgacaaggttctgatgattgttgtgttttgcag------------------------------
                  || ||  |||||||| | ||| ||||||||||||||||||  |||| |||||||||| |||||||| ||  | |||||||| | | | || | ||   |  |  |||   | |||  ||  ||  || |||  ||  ||   | | ||  |      |  |  ||          |  || || |                              
------------------CGCCGGCCTCCGCGTGCGCGTGCTCGGCTGGATCTGCGTCAGCGTCGCGCTCAGCGTATTCGCCGCGCCGCTCAGCATCATGgcacg-tatctaatttaatctctctctctctctctctctctc-tctctctctctctctctctgaagagggatgtgaattgttggaaccgccattaattcgctgactgccctatctacatctactttcctgcag

upper sequence: LOC_Os02g30910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G168365_T02 (Zea mays), 5'ss of exon 4
CACGCTGCTGCTCTCCCGCGGCGAGCTCCGCGTCCACGTCCTCGGCTGGATCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagcaaacgaatgcaatcttgatgtcttgctaactaatcgctcgatcgatcaaccagcagctgatgacaaggttctgatgattgttgtgttttgcag
|||  |||| ||||||  || ||  |||||||| ||||| ||||||||||||||||||  |||||||||||||||||||||||| ||  | ||||| || ||     |     |   |||  | | | |  |||  |   | ||   |  |  | |     | |     || |       || |  |      || || ||||
CACCATGCTTCTCTCCGACGCCGGCCTCCGCGTGCACGTGCTCGGCTGGATCTGCGTCAGCGTCTCGCTCAGCGTCTTCGCCGCGCCGCTCAGCATAATGgt--ttcattcttctgttgccttttggtttcctttgtctgttattagttaaatggtttgtaatcgttcaataaa------ctaactacctgcttgctt-gcag

upper sequence: LOC_Os02g30910.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G872392_T03 (Zea mays), 5'ss of exon 2
CACGCTGCTGCTCTCCCGCGGCGAGCTCCGCGTCCACGTCCTCGGCTGGATCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagcaaacgaatgcaatcttgatgtcttgctaactaatcgctcgatcgatcaaccagcagctgatgacaaggttctgatgattgttgtgttttgcag------------------------------
|||  || || ||||| ||| ||  |||||||| | ||| ||||||||||||||||||  |||| |||||||||| |||||||| ||  | |||||||| | | | || | ||   |  |  |||   | |||  ||  ||  || |||  ||  ||   | | ||  |      |  |  ||          |  || || |                              
CACCATGGTGGTCTCCAGCGCCGGCCTCCGCGTGCGCGTGCTCGGCTGGATCTGCGTCAGCGTCGCGCTCAGCGTATTCGCCGCGCCGCTCAGCATCATGgcacg-tatctaatttaatctctctctctctctctctctctc-tctctctctctctctctctgaagagggatgtgaattgttggaaccgccattaattcgctgactgccctatctacatctactttcctgcag

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|33794238|gb|CF323009.1|CF323009
EST:     CTG-GNTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATC                         AGGCTGGTGATCCGGACCAAGAGCGTGGAGTTCATGCCATTCTCGCTATCC
genomic: CTGCG-TCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagc ... tgttttgcagAGGCTGGTGATCCGGACCAAGAGCGTGGAGTTCATGCCATTCTCGCTATCC
EST: gi|33795226|gb|CF323485.1|CF323485
EST:     T-CGGTTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATC                         AGGCCTGGTGATCCGGACCAAGAAGCGTGGAGTTCATGCCATTCTCGCTAT
genomic: TGCG-T-CGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagc ... tgttttgcagAGGC-TGGTGATCCGGACCAAGA-GCGTGGAGTTCATGCCATTCTCGCTAT
EST: gi|33682452|gb|CF310691.1|CF310691
EST:     TCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATC                         AGGCTGGTGATCCGGACCAAGAGCGTGGAGTTCATGCCATTCTCGCTATCC
genomic: TCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagc ... tgttttgcagAGGCTGGTGATCCGGACCAAGAGCGTGGAGTTCATGCCATTCTCGCTATCC

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: 37 (upstream exon), 65 (downstream exon)
Score: 22

CACGCTGCTGCTCTCCCGCGGCGAGCTCCGCGTCCACGTCCTCGGCTGGATCTGCGTCGCCGTCTCGCTCAGCGTCTTCGCCGCTCCCTTGAGCATCATCgtaagctagc ... tgttttgcagAGGCTGGTGATCCGGACCAAGAGCGTGGAGTTCATGCCATTCTCGCTATCCTTCTTCCTGGTGCTTAGCGCGGTGATCTGGTTCTTGTACGGGCTGCTCA




<











<


<