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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------attttttaggctatctattttaatt-tattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttctttt---ctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
                                                            |||  | |||||| |  || | ||  |||  ||     | ||||||  ||| |    |||||||  || ||| | | ||    || |||||  |    |  ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || || ||||||
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctggattttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 18
attttttaggctatctat-tttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattt-taattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
     | |  |      | |    | || |  |   |  | || |||       | |||    || | ||   | | | |||   | |    |||| |  ||||| ||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | |||||||||||| ||
--caatgacacccctagtatcctgtctactttctcagcccactttttaaaacattgactgaatttgtcaagcatattaatgaaagattaccattttgtttagGAAGAAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 3'ss of exon 18
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
         | | | ||  | ||   ||||   |       |  || |    |  |    |    | |||| ||  || |  |     | |       ||||| |||||||| || ||||| || ||||||||||| ||||| || |||||||| || ||||| ||| | || || |  ||  || ||||||| || || 
---------gttttataaatcaaaacattcttgttatttctttctttgcggaagaaaaagt----tgaaatgtttgttaaaacttcaatgtgcatgacagGAAGAAGAACATATTTAAGTTGGCGCAAGGAGAATATATAGCACCAGAGAAGATCGAAAATGTTTATACCAAATGTAGATTCGTTTCGCAGTGTTTCATT

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 3'ss of exon 18
-attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttc--ttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
 |||  |||    |   | |||        |      |   |   ||    | || |  |||   |   | |     ||||||||       ||| |  || ||||||||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || || ||||| 
aattgcttacaaaagaaactttgtgaagagcaggaacatgccaactttaagttatgaaattttagtctcttagcgaaaattgatg--gccaacttatgaca-gGAAAAAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATC

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------------------------------------------------attttttaggctatctatttta------atttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
                                                                                          || | || | |     |||||       || || ||  ||  || |   |      | |    |    || |||  |||  ||| |   || ||  | |     ||||| ||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| ||||||||| ||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaa---aagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctca-agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
 | |  |  |      | ||||  || | |   |  |    ||||       | ||  ||   |  |   | ||  ||||  || |  ||     |   ||||| ||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||| |  |||
-tgtcgtgagtggatcaatttagcttttactttttcaggaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacacattgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
--------------------------------------------------------------------attttttaggctatctattttaatttattcccctggaactctgtttc--gtctgatt--acttttcttatt----aaattttaattgatgcaattttcttttctca--------agGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
                                                                     |   | ||  || | | || | | | |||  ||       ||||    |    ||   |||||   ||||     |  ||| ||   |   |  |||||| ||          || || ||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| |||||        |   ||| ||||| ||||||||||| 
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaactttgaatatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATT

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 3'ss of exon 20
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttct---tttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
|  |||||  ||   | | | ||  | |  |     ||   | | | |       | || |  |  | |  |||  ||  |    |||  |   | |||  ||||| ||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||| ||  ||
aagttttattct---tctctgaaactgtaactagaaaaaattatctggaagtggcagttcttatgctcatgtttgttttgtatcctttaatcactgtctgcagGAAGAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTA

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: EFJ37488 (Selaginella moellendorffii), 3'ss of exon 19
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
                                               ||    |   || | | |||  |||||  |||| |  |||||    |  | ||||||||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||   ||  |||||||  |||| ||||| ||  | 
-----------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcatttt----ttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 18
lower sequence: EFJ33980 (Selaginella moellendorffii), 3'ss of exon 19
attttttaggctatctattttaatttattcccctggaactctgtttcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
                                               ||    |   || | | |||  |||||  |||| |  |||||    |  | ||||||||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||  |||  |||||||  |||| ||||| ||  | 
-----------------------------------------------gtaacgtgctttgtgtcattcgattttgcttgacgtcatttt----ttgccagGAAAAAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTC

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|66919239|gb|CX106087.1|CX106087
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|58590451|gb|CF988759.1|CF988759
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|58595336|gb|CF993644.1|CF993644
EST:     GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAG                         GAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: GGAGACATAGGTTTGTGGCTGCCTGGAGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
EST: gi|29665943|gb|CB662218.1|CB662218
EST:     AGGGCGTTTAANAATTATAGATAG                         GAAAAAGAACA-TTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA
genomic: AGGGCGTTTAAAAATTATAGATAGgtaaaactga ... ttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtctgattacttttcttattaaattttaattgatgcaattttcttttctcaagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTGCTTTATA
                                     caattttcttttctc  CT-rich tract
       attacttttcttatta  TA-rich tract