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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g31290.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 1
gtatgtgtaacaactgt-taatttaggttcattt--ttttttcttgcctttgccttct-tttctgtcattttcatgtatttctaattgact---tgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
               || |  |||  | ||| |   |||| |  | | |||   |||| | ||  | |  ||  | |  ||||  ||| ||   | || || |||||| ||||| ||||||||  | |||||||||||||||| |||||| || |||||||||||||||||| | |||||||| || |||
---------------gtatgttttgagatcactcagttttatgctacatttatgttctgtctcaataaaatttcttttgttctggttggctcttttgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGATTTTATTTACTTGCCAATTGATTTTAAG

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 11
gtatgtgtaacaactgt-taatttaggttcattt--ttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgact---tgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
               || |  |||  | |||     |||| |  | | |||   |||| |      || ||| | | || ||  |||  |   | || || |||||| ||||| ||||||||  | |||||||||||||||| |||||| || |||||||| ||||||||| | |||||||| || |||
---------------gtatgttttgagatcaccaaattttatgctacatttatgttctgtctcaatatattcttttgtt-ctggttggttctttcgggtttcagGTATACCTCCAAGATGCTCTTGGCTGCTATTGATGAAAGTCATAAGGGCACTTATGACTTTATTTACTTGCCAATTGATTTTAAG

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 3
-gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttg--ggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
 || | |     || ||   | ||| ||||| || |    ||    |      | ||||||   |   || | | | |   | ||| |||  |  || |||||| || || ||||||||  ||||||| |||||||||   |||| ||| |||||||||||| |||| || |||||||| ||||  
agttttttctgaaaatgaagaattatgttcagttctacacctcatttacataattttttcttgaaacatctttt-tctgggactgatttgttgtcttgcagGTATACATCCAAGATGCTGTTAGCTGCAATTGATGAACGCCATAGAGGAACTTATGATTTTGTTTATCTGCCAATTGATTTCAGA

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
||| ||| |   ||  ||  |     ||  |   | |||  |  | ||   |  |  ||  |  ||   || | | | |  |    |   | ||  ||||| || || |||||||| |||||||||||||||||  |   |||||| || ||||||||| ||||  | |||||||||||||||
gtaagtgaattcaccttttctccctattattccctgttttataacattatatgttgctcatttgttcctatttgtctttgttctggtaatggttt-agGTATACTTCTAAGATGCTCCTAGCTGCTATTGATGAGTACTGTAAAGGAACATATGATTTTCTTTATTTGCCAATTGACTTCAAG

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------------gtatgtgtaacaactgttaatttaggttcatttttt------tttcttgcctttgccttc--ttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
                                             | || ||| | |  || |||  ||   |  ||       | |  ||  ||   |||    | ||| |  ||||  | | ||| |||||    |  | ||  |||||||| || |||||||||||| |||||||||| ||  ||  |||||| |||||||||||  ||||  | |||||||||||||||
gtacgtgaactcagtgtctctcttttatttttcttgtctatatcttctgcaactatttatagtttgtgtctttagttaaagatgtattctgttttcatctttgactctcttttttttttttttttttttaattctgctatggttt-agGTACACTTCGAAGATGCTTCTATCTGCTATTGACGAGCATTGTAAAGGAACTTATGATTTCCTTTATTTGCCAATTGACTTCAAG

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 11
gtatgtgtaacaact-gttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatt--tctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
  ||   |  | | | ||   ||||    |  |  ||  ||       ||     |  ||||| ||||     | ||  | | ||  | | |  |||  ||||| || ||||| |||||||| ||||| ||||||||| |||||  ||| |||||||||||||||||  | |||||||||||||| 
-cattcatttctatttgtggttttacacaccataattgctcagattcctgttgcatcctctgttatttctgccttttgatttgatataatggtaattgtagGTATACTTCAAAAATGCTTCTTGCTGCAATTGATGAACATCATCGAGGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 1
gtatgtgtaacaactgttaatttaggttcatttttttttcttgcctttgccttcttttctgtcattttcatgtatt--tctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
                                               ||     |  ||| | ||||     | ||  | | ||  | | |  |||  ||||| || ||||| |||||||| ||| | ||||||||| | |||  ||| |||||||||||||||||  | |||||||||||||| 
-----------------------------------------------tgttgcatcctctattatttctgccttttgatttgatataatggtaattataggtatacttcaaaaatgcttcttgctacaattgatgaacaccattgagGAACTTATGATTTTATTTATTTGCCAATTGACTTCAAA

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|58687890|gb|CK076577.1|CK076577
EST:     CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA                         GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
EST: gi|58691922|gb|CK080609.1|CK080609
EST:     CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA                         GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
EST: gi|56158059|gb|C72031.2|C72031
EST:     CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA                         GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
EST: gi|66930475|gb|CX117323.1|CX117323
EST:     CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAA                         GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC
genomic: CGTGGTGATGACTCCCGGACTACGCTGATGATAAAGAATATCCCAAACAAgtatgtgtaa ... gggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttgccttcttttctgtcattttcatgtatttctaattgacttgggattccagGTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG
                    attttcatgtattt  TA-rich tract