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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcatagctagttgacatatgttttaagcagttaagcacatgtgtatctagagtctgcgattaccaatttatcattgtaattaagtgttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT

Basic information

species Oryza sativa
transcript LOC_Os11g48090.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 5
tgagcatagctag--ttgacatatgttttaagcagttaagcacatgtgtatctagagtctg--cgattaccaatttatcattgtaattaagtgttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT
    |  ||||||  ||    ||    |  |||  |    | ||  |  |   | | |     | ||    ||||      || || | |  ||| ||||||||||||| ||||||||||| |||||||| ||||||||||| || ||||||||||||||||||||||| ||  | || |||||||||||||| ||||||||||
----ctcagctagggttactgtagcactgtagctctctctctcactttcaagcacaatggaatctatctataattgtcagctgcaaatgacagttctcatgcagGAGGCTCACTGCTGTAGCCAATGGGGTCATGATTTTCGTCCTGACTACAAGAATCTTGGCATTTTGAAAATTCAATTTCCCAGTGTTCCAATGATAGCTT

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 4
tgagcatagctagttgacatatgttttaagcagttaagcacatgtgtatctagagtctgcgatt---accaatttatcattg-taattaagtgttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT
   |  |  ||| ||    |||  || || ||||     |  |   || | |   | ||  | |   |  |   ||| |||  |  ||| |  ||    ||||||| ||||| ||||||||||||||||| ||||| ||||| || ||||||||||  ||  | ||| | |||   ||||| ||  ||||||||||  | ||||
---gactcactatttcctctatccttcaa-cagtctcagagtttcatagcaatgctgtgttagttgtatgacaatataattcctggttatggtttgcattgcagGAAGCACATTGCTGTAGTCAATGGGGTCATGACTTTCGACCTGACTACAAGAGCCTCAGTATTCTCAAGACACAGTTCCCTCGTGTTCCTATTGTTGCTT

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------tga-gcatagctagttgacatatgttttaagc--agttaagcacatgtgtatctagagtctgcgattaccaatttatcattg--taatt----aagt---gttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT
                                            ||   | || ||  |     | ||  || ||   | ||    | ||  | | |   |  | |  |   | | ||||| | ||   ||||    | ||   |||    |||||||||| || || |||||||| ||||| |||||||||||||| || ||||||||  |  ||||| | ||   |||||||||||  ||||| ||| | ||||
gtaagtctctcctagttttagtttcttactcggaaattgtgctctgccacctatcttctcactctctggctttagtttatttggatatatccgcaccgttaaacagaaaac-ctactttatgaatgatcaatttcctatgtttggtttctttgcagGAGGCTCATTGTTGTAGTCAGTGGGGTCATGATTTTCGCCCTGATTACAAGAACTTAAGCATTCTGAAAACCCAGTTTCCCAAAGTTCCCATGGTGGCTT

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 4
-----tgagcata--gctagttgacatatgttttaagcagttaagcacatgtgtatctagagtctgcgattaccaatttatcattgtaattaagtg-ttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT
     | |  ||       ||| ||  ||| ||| |    ||  |||  | | |||   ||  ||||       | | | | ||  |||||   || ||    | ||||||||||| ||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||| ||||||   ||||||||   ||||||  |  | ||||
ctttttcattatgttatctgtttac-catggttttattttttgggcatttatatat---gaagctgcagg----actgtgtaatgttaattctttgattgctttacagGAGGCACATTGCTGTAGTCAGTGGGGCCATGACTTTCGCCCAGATTACAAAAATCTTGGCATCTTAAAGACTCAGTTTCCTGATGTTCCAGTAGTTGCTT

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|58672003|gb|CK060689.1|CK060689
EST:     AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGAT                         GAGGCACACTGCTGTAGT
genomic: AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGATgtgagttttt ... tatcatgcagGAGGCACACTGCTGTAGT
EST: gi|58671155|gb|CK059841.1|CK059841
EST:     AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGAT                         GAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGGCCAGACTACAAG
genomic: AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGATgtgagttttt ... tatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG
EST: gi|58661067|gb|CK049747.1|CK049747
EST:     TTCTCTCATTGCAATAGAT                         AAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG
genomic: TTCTCTCATTGCAATAGATgtgagttttt ... tatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG
EST: gi|58690628|gb|CK079315.1|CK079315
EST:     AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGAT                         GAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG
genomic: AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGATgtgagttttt ... tatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG
EST: gi|29673292|gb|CB669567.1|CB669567
EST:     AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGAT                         GAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG
genomic: AGCTTGAGAAATGCCACCATGCAGGGCGTCTTTCTCTCATTGCAATAGATgtgagttttt ... tatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctagagtctgcgattaccaatttatcattgtaattaagtgttatcatgcagGAGGCACACTGCTGTAGTCAATGGGGCCATGATTTTCGCCCAGACTACAAGAATCTTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTT
                      aatttatcattgtaat  TA-rich tract