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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgagagccgaagcggcggcggctgcattgcattttttcctgctcgggatttcgcattctgaatccacgtcttggatttttgctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACGT

Basic information

species Oryza sativa
transcript LOC_Os01g55500.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G437859_T03 (Zea mays), 3'ss of exon 1
gtgcgtgagagccgaagcggcggcggctgcattgcattttttcctgc-tcgggatttcgcattctgaatccac-----gtcttgga-----tttttgct----gtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACGT
    ||| |  || ||||    |  |||| |  |  ||     | || | || |||  |   ||||||||        || || |      ||||||||     ||||||| ||||||||||||||||| |||||||||||||| |||||||||||||||||||||||||||||| | ||| |||| ||||||||||||||   |||   
----gtgcgtacccaagc--ttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGGCGGTGATGATCCCGACAGTGTTGGTTCCCATGATGGGCGGCGACGAT--
















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|88355309|gb|CI679012.1|CI679012
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
EST: gi|88583644|gb|CI701146.1|CI701146
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
EST: gi|88361794|gb|CI681954.1|CI681954
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
EST: gi|88391930|gb|CI683748.1|CI683748
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
EST: gi|88591374|gb|CI707404.1|CI707404
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCCGCCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
EST: gi|88577986|gb|CI674609.1|CI674609
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
EST: gi|88731891|gb|CI753401.1|CI753401
EST:     GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG
genomic: GGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGG

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: 33 (upstream exon), 65 (downstream exon)
Score: 5

GCGGCGACGATGGCTGAGGTGAAGCCGGAAGAGATCAGCTACCCGCCCATGGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgaga ... gctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACGT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgctcgggatttcgcattctgaatccacgtcttggatttttgctgtttcagGGGAGGCGATCATACTGGGATTCCAGCACTACATCCTGGCGCTGGGCACGGCGGTGATGATCCCGGCGGTGCTGGTGCCCATGATGGGCGGGAGCGACGT
                                        tttttgct  CT-rich tract
                                       attttt  TA-rich tract