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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcacttttcccccaacaatttctttatgtcctcaaagtttcttataagcatctatttcttgtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG

Basic information

species Oryza sativa
transcript LOC_Os11g17080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G38510.1 (Glycine max), 3'ss of exon 2
-----------------gtatatcacttttcccccaacaatttctttatgtcctcaaagtttcttataagcatctatttcttgtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG
                  |  |  |||   ||  |||||     ||  | |  |||   |   || |      | | || || |  ||  ||||||| |||||||||||||||||| | || |||||| | |||||||| |||||||| |||
gtaagaatcttttgcctctgaaatactca-ccttcaacatagctttcctcttgtcatcatgcattgtttatgcccacttgtt-tccttgcagGATTACGTTGCAACAAGGTGGTATAGAGCTCCTGAATTGTGTGGATCCTTTTTCTCCAAG

upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G02220.1 (Glycine max), 3'ss of exon 3
-----------------gtatatcacttttcccccaacaatttctttatgtcctcaaagtttcttataagcatctatttcttgtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG
                   | |  |||   ||  |||||      |  | || |||   |   || |      | | || || |  ||  |||||||||||||||||||||||||| | || |||||| | |||||||| |||||||| |||
gtaagaatcttttgcctccaaaatactca-ccttcaacatagctctcctctcgtcatcatgcattgtttatgcccacttgtt-tccttgcagGATTATGTTGCAACAAGGTGGTATAGAGCTCCTGAATTGTGTGGATCCTTTTTCTCCAAG

upper sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------gtatatcacttttcccccaacaatttctttatgtcctcaaagtttcttata-----agcatctatttcttgtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG
                                                                       |  |    | |     || |||    ||      | ||  | |||   |     ||| |  ||||| |||  ||  |||||||||||||||||||||||||  | ||||||||| | ||||| || |||||||| |||
gtatgcttcttccccatttgtgtgtgtttcttgtcaatcaattgcaatggtctatttttctttgtgacttaaagttgtgtatgggtaaataatgatgtttccctatgaatatctctagaattgacagctttaatttcatgtgattacagGATTATGTTGCAACAAGGTGGTACAGGGCACCTGAATTGTGTGGTTCATTTTTCTCCAAG

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|117237171|gb|CT861779.1|CT861779
EST:     GCCTTGCAAGAGTTGCTTTCAGTGATACACCAACTGCCATCTTTTGGACG                         GATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTT
genomic: GCCTTGCAAGAGTTGCTTTCAGTGATACACCAACTGCCATCTTTTGGACGgtatatcact ... gtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTT
EST: gi|58600533|gb|CK011061.1|CK011061
EST:     GCCTTGCAAGAGTTGCTTTCAGTGATACACCAACTGCCATCTTTTGGACG                         GATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTT
genomic: GCCTTGCAAGAGTTGCTTTCAGTGATACACCAACTGCCATCTTTTGGACGgtatatcact ... gtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttctttatgtcctcaaagtttcttataagcatctatttcttgtatttttagGATTATGTTGCAACAAGGTGGTATCGTGCACCTGAACTTTGTGGATCTTTTTTCTCTAAG
                                       tttcttgtattttt  CT-rich tract
                                     tatttcttgtattttt  TA-rich tract