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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtccccccctctcctgcttggctagggtttctgcggctcttttgctcacccgcctgcgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os05g30800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G467059_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------gtgcgtccccccctctcctgcttggctagggtttctgcggctcttttgctcacccgcctgcgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                                                              || |||| |  |  | || ||||   |  |   || | | ||     |      ||       | ||||||||||||||||||||| |||||||| ||||| || ||||| || ||||||||||| |||||||| |||||||| ||||||||||||||||||||||||||
gtgcgtagatcctccctctcttccccgtcccttccctgtaaccctagggtcagggactcagggttcgtctctgctccccccgctttcgttcgcgctcggggactgacgcgtggtttcggacttcggtcgcagGGAGGGCCGGCGTGCCCATGGAGGTCATGGGTCTCATGCTCGGCGAGTTCGTCGATGACTACACCGTCAGGGTCGTCGACGTCTTCGCCATGCCGCAGAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033626_T01 (Zea mays), 3'ss of exon 1
--------------------------------------gtgcgtccccccctctcctgcttggctagggtttctgcggctcttttgctcacccgcctgcgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                                        | || |  |||| |  | ||| |||   | |   ||      | || |    ||  | || |  ||||||||||| || ||||| |||||||| ||||| || ||||| || |||||||| ||||||||||| |||||||| ||||||||||||||||||||||||||
gtgcgtggatcctccttccctcccccggaatctagggttagggttcgtccctgttttcctttgctttcgctcgcgctcggggtctgatgcgtcgttt-cg-gttgcagGGAGGGCTGGGGTGCCCATGGAGGTCATGGGCCTCATGCTCGGCGAGTTCGTTGACGACTACACCGTCAGGGTCGTCGACGTCTTCGCCATGCCGCAGAG

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP09161 (Chlamydomonas reinhardtii), 3'ss of exon 2
------------------------------------------------------------------------------------------------------gtgcgtccccccctctcctgcttg--gctagggtttctgcggctctt---ttgctcacccgcctgcgc--------------gccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                                                                                                        || ||  | ||   | ||||||   |  | |   | || ||||||   |    ||||||||  | |              ||   |||  | ||||| ||||| |||||||| ||||| || ||| |||| ||||| || ||||||||||||||  ||||||| ||||| || || |||||||||  
gtaaggcgccgtgtttgcttgggtcctctgatagtagtgatgatgctacatcctggaggccgaccgcgagcgcttgaaggccctgcgctgcgaccccgtgtccagcttcggcacccagcttgcttgcaacccgtgcaccagcagctcttcaatcatccacccgcccactctgcccgcaacctttgcaatagGCCGCGCCGGTGTGCCCATGGAGGTCATGGGCCTCATGTTGGGCGAGTTTGTGGACGACTACACGGTGCGGGTGGTGGACGTGTTTGCGATGCCGCAGTC

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------gtgcgtccccccctctcctgcttggctagggtttctgcggctctt-ttgctcacccgcctgcgcgcc---gcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                            |  |        ||    ||| | | ||    ||  |  ||   ||| | ||     ||  ||     ||||| || || || ||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||| ||  | || || || || || || ||||| |||||
tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG

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|29615551|gb|CB620563.1|CB620563
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|58599931|gb|CK010459.1|CK010459
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|58681730|gb|CK070417.1|CK070417
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|163919983|gb|EG714925.1|EG714925
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|58686484|gb|CK075171.1|CK075171
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|88826224|gb|CI776789.1|CI776789
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|15008261|gb|AU222649.1|AU222649
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|29620645|gb|CB625656.1|CB625656
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|218498489|gb|FG961937.1|FG961937
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
EST: gi|117227458|gb|CT846600.1|CT846600
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCG

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), 74 (downstream exon)
Score: 14

GCCTCCGGCATGGGGCAGCCGCCGTCGGACTCGCCGCTGCTCGACTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtgcgtcccc ... cgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgcttggctagggtttctgcggctcttttgctcacccgcctgcgcgccgcagGGAGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTGGGGGAGTTCGTCGACGACTACACGGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                               tgctcac  putative branch site (score: 14)