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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccccgccgccgcccccccctcctctcgatcctcgcgttcgatccgtccgccggttttgttttttagggtttggaattgcagcgatctggtcccccgatctggtttggttatggaaggggatgggtttttggtccttattgcggttggtgtgcttcgtgtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC

Basic information

species Oryza sativa
transcript LOC_Os03g48930.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g48930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G097164_T02 (Zea mays), 3'ss of exon 1
gtaagacccc-gccgccgcccccccctcctctcgatcctcgcgttcgatccgtccgccggttttgttttttagggtttggaattgca-gcgatctggtcccccgatctggtttggttatggaaggggatgggtttttggtccttattgcggttggtgtgcttcgtgtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC
||| |  | | |||  ||||   || | |  || |    ||    | |||  | |  || |    |||||| || ||| |  |  |  |||||||| || |  ||||||  | ||||           ||||     ||| || |||| ||  |      ||  |||   ||||||||||| || || |||||||| |||||||| ||||||||||| |||||||| |||| ||||||||||   ||||||||| ||||||| ||||| ||||||
gtaggttctctgccctcgccgatccgttcgttcaaaggccg--gcctatcgattccacgttcgctttttttgggtttttgtgtgtcgtgcgatctgatctc--gatctgcctgggtttc---------tggg-----ggttctgattggggccg------tttctgttggcgcagGGTGCAATTTACGGAGTTCATACAGAAGAACCTCCACCTGTACCAGTTCCGGAACACCATCCCGCTCTCAACCGCCGCCGCCGCCAACTTCACACGCGGC

upper sequence: LOC_Os03g48930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G111566_T01 (Zea mays), 3'ss of exon 1
gtaagaccccgccgccgcccccccctcctc-tcgatcctcgcgttcgat--ccgtccgccggttttgttttttagggtttggaattgcagcgatctg-gtcccccgatctggtttggttatggaaggggatgggtttttggtccttattgcggttggtgtgcttcgtgtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC
             |  |     ||  ||||  ||||||   |||||||   | | ||  || ||   | ||  |   | | |  ||       | || ||  | ||||||| |   | | ||        ||||||| ||       ||  | |||| |   ||  |||   |||||||||||||| || |||||||| |||||||| ||||||||||| ||||||||||||| |||||||||    ||||||||  ||||||| ||||| ||||||
-------------gtaggttttccgccctcgccgatccgttcgttcgacggctggccatcgattccatgttcgactttctagggttttttttttgtgtgttgcgcgatctgatgccgatctgcc------tgggtttctg---tgagttctgattggaggcgtttctgttggcgcagGGTGCAGTTTACGGAGTTCATACAGAAGAACCTCCACCTGTACCAGTTCCGCAACACCATCCCGCTGTCAACCGCCGCTGCCGCCAACTTCACACGCGGC

upper sequence: LOC_Os03g48930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G38970.1 (Glycine max), 3'ss of exon 1
gtaagaccccgccgccgcccccccctcctctcgatcctcgcgttcgatccgtccgccggttttgttttttagggtttggaattgcagcgatctggtcccccgatctggtttggttatggaaggggatgggtttttggtccttattgcggttggtgtgcttcgtgtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC-------
                                                         |  | |  | | ||||||| ||  ||        ||  || ||   |||  |    |                  | || |||        |||  | | | |  ||| ||   ||||| |||||||| |||| ||| ||||||||  ||  | ||||||||||||| |||  |||||| || | |||||||||| ||||||||||||| || |||       
---------------------------------------------------------gtatctactatctagggttagggttt--------cttctctcctactctcttccaatc----------------ctctgatccc-------gttcctttccgttctgtttt---agggttcagTTCACAGAGTACATTCAGAAGAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTTACCACCGCCGCCGCCGCCAATTTCACGCGTGGCGAACTCG

upper sequence: LOC_Os03g48930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G44200.1 (Glycine max), 3'ss of exon 1
gtaagaccccgccgccgcccccccctcctctcgatcctcgcgttcgatccgtccgccggttttgttttttagggtttggaattgcagcgatctggtcccccgatctggtttggttatggaaggggatgggtttttggtccttattgcggttggtgtgcttcgtgtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC
                                                                                             |   |  | |||| |   | ||| ||       |       |       | | |  ||       | | |    |   ||||| || ||||| |||| ||| ||||| ||  ||  | ||||||||||||| |||  |||||| |||| |||||||||| ||||||||||||| || |||
---------------------------------------------------------------------------------------------gtatctactatctag---gcttagggtttcttctctcccactctcttccaatcctcttatccccttcctttctcttttagGGTTCAATTCACTGAGTACATTCAGAAAAACGTCGCCTTGTATCAGTTCCGTAACGGCATCCCTCTCACCACCGCCGCCGCCGCCAATTTCACACGTGGC

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|88329763|gb|CI651427.1|CI651427
EST:     AGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: AGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|428606|gb|D24758.1|D24758
EST:     AGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: AGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|58685422|gb|CK074109.1|CK074109
EST:     GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|88339390|gb|CI635368.1|CI635368
EST:     GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|29659834|gb|CB656109.1|CB656109
EST:     GTGCTGGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|86824114|gb|CI260755.1|CI260755
EST:     TGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: TGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|88349785|gb|CI632920.1|CI632920
EST:     GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
EST: gi|33678293|gb|CF306532.1|CF306532
EST:     GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCG                         GGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG
genomic: GTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCG

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: 74 (upstream exon), 73 (downstream exon)
Score: 77

CGGCGGTGCAGAGCATCCTGGTCCACAAGACCGACGAGGACAAGGTGATGGTGCTCGACAGCCACAAGCTGATGGGCGCGTCCGGAGAGCCCGGCGACCGgtaagacccc ... gtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaggggatgggtttttggtccttattgcggttggtgtgcttcgtgtgttcgcagGGTGCAGTTCACCGAGTTCATCCAGAAGAATCTCCACCTGTATCAGTTCCGCAACAACATCCCGCTCAGCACCGCCGCCACCGCCAATTTCACCCGCGGC
            ttttt  TA-rich tract