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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCCTCCCGGCCGCGCCATGGTGAGGCTCACCGCCGACCTGATATGGAAGAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgctctttcctccctgctcgctagatctagggtttagtgttcttggccctcttttttcattccctccgtctcggtagtttaatttgtctgttgtgtttcttttccttggcag

Basic information

species Oryza sativa
transcript LOC_Os02g13990.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G021742_T01 (Zea mays), 5'ss of exon 1
CGCCCTCCCGGCCGCGCCATGGTGAGGCTCACCGCCGACCTGATATGGAAGAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgctct-ttcctccct--gctcgctagatctagggtttagtgttcttggccctcttttttcattccctccg----tctcggtagtttaatttgtctgttgtgtttcttttccttggcag
||||  | |     ||||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||| | |||  ||||| |||   |  | |||||||||||||  ||||| ||  |         |||   ||   |    ||    |  |  || ||  |||  |                   
CGCCTCCTCCCAGTCGCCATGGTCAGGCTCACCGCTGACCTGATATGGAAGAGCCCGCACTTCTTCAACGCCGTCAAGGAGCGCGAGCTCGACCTCCGAGgtttgcccactcccttccttcctccacctgttagatctagggttatgtgttattctcttcgaaagctcacggcccttgctcttcctcctcctccaacttcgctgcag-------------------

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 5'ss of exon 1
CGCCCTCCCGGCCGCGCCATGGTGAGGCTCACCGCCGACCTGATATGGAAGAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgctctttcctccctgc-tcgctagatctagggtttagtgttcttggccctcttttttcattccctccgtctcggtagtttaatttgtctgttgtgtttcttttccttggcag
 | |  ||       |  |||||||||||||| || |||||||| ||||| ||||| || |||||||| ||| ||| ||| || ||  | ||  | |||||| | |  |  || |||  | | | |  ||| || |         | ||||   |  || ||   |    |   ||   |  ||||| | ||     |  ||                  
TGGCTGCCGAAGAAAGAGATGGTGAGGCTCACTGCAGACCTGATTTGGAAAAGCCCTCATTTCTTCAATGCCATCAGGGAGCGAGAATTGGATCTTCGAGgtattccagtcctgtcccgctttcatttctacattt-----cctctattctaatcattccttcccccaaactaacggaaccctagttcacttcacacgaagttac---------------
















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|218492413|gb|FG947005.1|FG947005
EST:     GAGCCCGCACTTCTTCAACGCCGTCAATGACCGCGAGCTCTACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|86904173|gb|CI306591.1|CI306591
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|29660695|gb|CB656970.1|CB656970
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|27553936|gb|CA997836.1|CA997836
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|88406774|gb|CI603968.1|CI603968
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|88445434|gb|CI584547.1|CI584547
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|86891922|gb|CI310086.1|CI310086
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|58602112|gb|CK012640.1|CK012640
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|88745945|gb|CI769305.1|CI769305
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|29663404|gb|CB659679.1|CB659679
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|88740329|gb|CI763837.1|CI763837
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|88400407|gb|CI593482.1|CI593482
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|38473912|gb|CF958044.1|CF958044
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|58662231|gb|CK050911.1|CK050911
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
EST: gi|5005008|gb|AU068325.1|AU068325
EST:     GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAG                         GTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG
genomic: GAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG

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: 70 (upstream exon), 68 (downstream exon)
Score: 81

CGCCCTCCCGGCCGCGCCATGGTGAGGCTCACCGCCGACCTGATATGGAAGAGCCCGCACTTCTTCAACGCCGTCAAGGACCGCGAGCTCGACATCCGAGgtttgcgcgc ... tccttggcagGTAACAAGATCCCCATCATCGAGAATCTGGGCGCCACCGAG




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