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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctacaccacaattgttcctgaacaatttaagcccctttcttttttgcattttaacagcttgtgtctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA

Basic information

species Oryza sativa
transcript LOC_Os05g05780.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 14
gtatgctacac-cacaattgttcctgaacaatttaagcccctttcttttttgcattttaac--agcttgtgtc-tattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
||||| |   | ||| ||  |   || |   |||| |    |   |   |  |||    ||  |||| | ||   ||| ||| | ||||||||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||||| |||||||| ||||||||||||||||||||||| |
gtatgtttttctcaccatgttatgtgta---tttatgtatttgagtacatgacatggctactaagctggagttacattccagCTTTGCATGGTGCACAAACTTGGATATGGAAACTGGGATGAACTGAAAGCTGCCTTCCGTATGTCTCCCTTGTTTCGATTTGATTGGTTTGTGAAGTCCA

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 22
-----------------------------gtatgctacaccacaattgttcctgaacaatttaagcccctttctt--ttttgcatttt---aacag----cttgtgt---cta--------------ttacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
                              | |||   |   || || ||  ||  ||  || ||  ||||  ||  | | |  ||||   |||||    |||||||   ||               || ||| |||| ||| | |||||||| || || || || ||||||||  |||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||| 
gtgtgaattttatttccttttgtttttatttttgcccaaattcatttctttttgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttgtgttgtctgactttacttaaaacttgcagATATGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGTTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 22
gtatgctacaccacaattgttcctgaacaatttaagcccct--ttcttttttgcatttt--aacagcttgtgtcta--ttacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
            |||||| ||  |      | ||   || |  | ||| | ||  |||   || |  |||     |  |||||| ||||||||||||||||||| || || || |||||||||||  | || ||||| ||||| |  || |||||||| ||||||||||||||||| || ||| 
----------gtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 22
-----------gtatgctacaccacaattgttcctgaacaatttaagcccctttctttttt----gcattttaacagcttgtgtcta--ttacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
            | |  | ||      || ||| |      | ||   || |     || |    |  | | || |  |||     |  |||||| ||||||||||||||||||| || || || |||||||||||  | || ||||| ||||| |  || |||||||| ||||||||||||||||| || ||| 
gtacaaattttatgtctttcaattttttttttctttctaggtctagctccatcatccttctatcggtttctaaaaaaattgctataaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCAGCATTTCGAACATCACCCTTGTTTCGATTTGATTGGTTTGTCAAATCTC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 22
---------------------------------------------------------gtatgctacaccacaattgttcctgaacaatttaagcccctttcttttttgcattttaacagcttgtgtctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
                                                          | | |    ||    ||  ||  |     |   | |    |||||   ||  || | ||  |   |     || ||| | || ||| | |||||||| || || || || |||||||| ||||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||| 
gtgtgaaatttatttccttttgtttttatttttgcccaaatttatttcttttcgttcatgttcagttccttgtttagtctggtgttttccgaacagaattcttg--tgttttctgacttcacttaaaacttgcagATTTGTATGATTCACAAACTTGGCTATGGTAATTGGGATGAGCTGAAGGCAGCTTTTCGAATGTCGCCCTTGTTTCGATTTGATTGGTTTGTCAAGTCTC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 22
------------------------gtatgctacaccacaattgttcctgaaca---atttaagcccctttcttttttgcattttaacagctt-gtgtctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
                        || || |  |  |||| ||||  ||        ||| |       ||||    |  | || |   ||   |   |  |  || |||||||||| |||||||| ||||| || ||||||||||| ||||| ||||| |||||||  || |||||||| || |||||||||||||| |||||| 
gtgagaattgcaatcatctctctagtttgtttgat-acaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtagATATGCATGGTTCACAAACTTGGATATGGGAACTGGGATGAGCTGAAGGCAGCATTTCGCACTTCTCCCTTGTTTCGTTTTGATTGGTTTGTAAAGTCTC

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|218491071|gb|FG964087.1|FG964087
EST:     ATGGCCAGAATAAAGGGAAG-T-TACAACGAAGAATGTGATCGTTTTATG                         TTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
genomic: ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
EST: gi|29632572|gb|CB637581.1|CB637581
EST:     ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATG                         TTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
genomic: ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
EST: gi|218488523|gb|FG953156.1|FG953156
EST:     ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATG                         TTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
genomic: ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
EST: gi|58599180|gb|CK009708.1|CK009708
EST:     ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATG                         TTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
genomic: ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
EST: gi|27577440|gb|CB000135.1|CB000135
EST:     ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATG                         TTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
genomic: ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
EST: gi|86831000|gb|CI295496.1|CI295496
EST:     ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATG                         TTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA
genomic: ATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCA

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), 69 (downstream exon)
Score: 50

GAAAAAGCTAGACCGCTATAAGAACCCTTGGTTAGAGTTGAAAATTCAGTATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctaca ... tctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacaatttaagcccctttcttttttgcattttaacagcttgtgtctattacagTTATGCATGGTGCACAAACTCGGATACGGAAACTGGGATGAACTGAAAGCAGCCTTTCGCATGTCGCCCTTGTTCCGATTTGATTGGTTTGTGAAGTCTA
                              ttttaac  putative branch site (score: 50)
                     ttttttgcattttaa  TA-rich tract