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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGGCCGTGCGGGCGGCGCCATGGCCAACCTCCAGCGCGGCGTTGGCTCCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctactcctactctagctccatatggatatggattcgattagctgtctacattctatgccatcaatttgttttccatcacttctcattatacatc...

Basic information

species Oryza sativa
transcript LOC_Os01g01010.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01010.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G031043_T01 (Zea mays), 5'ss of exon 1
CGGTGGCCGTGCGGGCGGCGCCATGGCCAACCTCCAGCGCGGCGTTGGCTCCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctactcctactctagctccatatggatatggattcgattagctgtctacattctatgccatcaatttgttttccatcacttctcattatacatc
||| |||||  |||||||||||||||||| |||||| ||||| || |||||||| || ||||||||  |||||||||||||||| || ||||| |||||||||   ||| |   || ||      | ||   |   |    | ||||  ||    | | ||| | ||  ||| | ||   |                   
CGGCGGCCGCCCGGGCGGCGCCATGGCCAGCCTCCACCGCGGGGTGGGCTCCCTTGTTCGTGACATCAGCGACCCCTGCCTCAATCCCTCCCCAGTTAAGgttg--ctattg--acccttatagtaaattagttctg--ctgtttagtagta-gtactatatactatggatt-gcttgatag------------------
















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|88327726|gb|CI657768.1|CI657768
EST:     CCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTCTGATAATGAT
genomic: CCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCC-GTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|88341250|gb|CI640007.1|CI640007
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|88851514|gb|CI670954.1|CI670954
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|88308051|gb|CI647878.1|CI647878
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|88571669|gb|CI663042.1|CI663042
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|88324962|gb|CI644973.1|CI644973
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|29675456|gb|CB671731.1|CB671731
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
EST: gi|88307292|gb|CI641930.1|CI641930
EST:     CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAG                         GGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT
genomic: CCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGAT

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: 38 (upstream exon), 73 (downstream exon)
Score: 8

CGGTGGCCGTGCGGGCGGCGCCATGGCCAACCTCCAGCGCGGCGTTGGCTCCCTCGTCCGTGACATTGGCGACCCCTGCCTCAACCCATCCCCCGTTAAGgttcgcctac ... aattgtgcagGGGAGCAAAATGCTCAAACCGGAAAAATGGCACACATGTTTTGATAATGATGGAAAGGTCATAGGTTTCCGTAAAGCCCTAAAATTCATTGTCTTAGGG




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