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

GGGGACTTGCTACATCACCCCCCTTCTCGGTGCCTTCTTGGCTGATGCCTACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatcgtcttggatttcagtttctgattgctatgatcgatggtgtgatcgaagagagagatgttttgatggttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g04950.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04950.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G020484_T08 (Zea mays), 5'ss of exon 3
GGGGACTTGCTACATCACCCCCCTTCTCGGTGCCTTCTTGGCTGATGCCTACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatcgtc--ttggatttcagtttctgattgctatgatcgatggtgtgatcgaagagagagatgttttgatggttgcag-------------
 ||||| ||||||||||| || ||  |||| |||||||| || || || |||||||| |||||||||||||| |||| ||||||||||||||||||  | ||||   ||||||  | | ||  ||   ||  ||||| ||       || |    |       | ||      ||| |   ||              
AGGGACGTGCTACATCACGCCGCTCATCGGCGCCTTCTTCGCCGACGCGTACATGGGGAGGTTCTGGACCATCGCCATCTTCATGATCATCTACATTTTCgtaa--gatcgtcgctcgaatccca---tcccattgccatccgacgaggagaagacaccacctgtgactgacggatcgactcaactgaactgaacag
















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|29631591|gb|CB636600.1|CB636600
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
EST: gi|29646409|gb|CB651416.1|CB651416
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
EST: gi|58690132|gb|CK078819.1|CK078819
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
EST: gi|117229908|gb|CT846338.1|CT846338
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
EST: gi|58664808|gb|CK053494.1|CK053494
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
EST: gi|29661642|gb|CB657917.1|CB657917
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCG
EST: gi|58673905|gb|CK062591.1|CK062591
EST:     ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTG                         GGGTTTGGGCGTTGCTTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCG
genomic: ACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGG-TTTGG-CGTTGCT-GACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCG
EST: gi|88400151|gb|CI590841.1|CI590841
EST:     CATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCCTG                         GGTTTGGCGTTGGTGACAATGGCGTCGTCGGTGAAGGGGC
genomic: CATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCC-TGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGC

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), 72 (downstream exon)
Score: 20

GGGGACTTGCTACATCACCCCCCTTCTCGGTGCCTTCTTGGCTGATGCCTACATGGGCAGGTTCTGGACCATTGCCAGCTTCATGATCATCTACATCCTGgtaactaatc ... atggttgcagGGTTTGGCGTTGCTGACAATGGCGTCGTCGGTGAAGGGGCTGGTGCCGGCGTGCGACGGAGGAGCGTGTCACCCGACGGAGGCGCAGACGGGGGTGGTGT




<











<


<