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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatttcagtgttttttgtctttctggcgtcacaattatgacaccctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA

Basic information

species Oryza sativa
transcript LOC_Os03g30260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 3
---------------gtaagtcatttcagtgttttttgtctttctggcgtcacaat------------tatgac---accctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                |||    ||    ||  ||||  ||| ||     || |||            | ||||   | | || ||    ||| |||||||||| ||||||||||||||||||||||| || ||| ||||||| ||| | || | ||| ||||| || || ||||| || || ||  | ||| | ||   
ccatacgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATAACAATACAGTTGTACC

upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 3
---------------gtaagtcatttcagtgttttttgtctttctggcgtcacaat------------tatgac---accctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                |||    ||    ||  ||||  ||| ||     || |||            | ||||   | | || ||    ||| |||||||||| ||||||||||||||||||||||| || ||| ||||||| ||| | || | ||| ||||| || || ||||| || ||  |  | ||| | ||   
ccatatgggatctaaataaacagttgttctgagtttttacttcctactagcaaaatccatcaacttagtttgaccttaacattgctctgatttattgcagTGACATGGAATGTGACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGTGTCTCGCTCTCATCTTTCTATGACAATACAGTTGTACC

upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 3
----------------------gtaagtcatttcagtgttttttgtctttctggcg-------tcacaattatgacaccctttcttcctttttttg-cagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                         |||  ||      ||||   || | || ||        |||   |  |   |||| ||  ||   ||| || ||||||| |||||||| |||||||||||||| || ||| ||||||| ||| | || | ||| || || || |||||||| || || || || ||  | ||   
ttatccgaaaagggtccaagttaacagttgttctgagtttttagttcctactagcaagatccatcaacttagtttgacccattgctctgatttatggcagTGACATGGAATGTAACATGCACATATTCACAATTTCTTGCTCAGAGAACACCCAGTTGCTGCGTCTCGCTTTCATCTTTCTATAACGATACTGTTGTACC

upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 3
--------------------------gtaagtcatttcagtgttttttgtct--ttctggcg--tcacaattatgacaccctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                            |  |  | | |||   | |       |||||||   | || ||    | | | |  ||    ||| |||||||||| |||||||||||||||||||| || || ||| | ||||||| | ||||  |||||||||| ||||||||||| || || ||||| ||  | |||  
gcttaaatttaaaacaattgaagtttacagttggtattagtaactatcagaaaattctggcaatttactatatccataacatcactcttgtttattgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAAAAAACTCCCTCTTGTTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 3
---------------------gtaagtcatt-tcagtgttttt---tgtctttctggcgtcacaat-tatgacaccctt----tcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                     | || | |   |  ||   | |   | ||         |  |||| | | | | ||||    ||     |||||||||||||| |||||||||||||||||||| || || ||| | ||||| | | ||||  |||| ||||| ||||||||||| || || ||||| ||  | |||  
gtgcttaaatttaaaacaactgaaaattacagttggtacctgtaactatcagctaattctagcaatctgttatatccttaacatcacttgttttttgcagTGACATGGAATGTGACATGCACATACTCACAATTTCTGGCTCAGAAAACTCCCTCTTGCTGTGTCTCACTTTCATCTTTCTATAATGATACCCTTGTTCC

upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G60920.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------gtaagtcatttcagtgttttttgtc-tttctggcgtcacaattatgacaccctttcttcctt---tttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                                |||  |||     |  ||    |  |||||    | |||     |  |    ||  || ||   ||  ||||||||| |||||  | || |||||||| ||||||||  ||||||||||| |||||||||| ||||||||  | || || || |||||||| || || |||  
gtaagaacccatgactgcaattcgacattttttaaaccataatgttagttaacattgtttctcatctaacagaccggttaaatgtttctctttgaattactgcagTGACATGGAACATTACGTGCACATACTCGCAGTTCCTTGCTCAAAGAACTCCAACTTGCTGTGTTTCTTTATCTTCTTTCTACAATGAAACCATTGTTGG

upper sequence: LOC_Os03g30260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G02210.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------gtaagtcatttcagtgttt-tttgtctttctggcgtcacaatta-tgacaccctttcttcctttttttgc------agTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                 | |    |  ||       |||| ||||   | |  |  |  | |||         || |||||| |||      ||||||||||||||| || |||||||| ||||||||  | ||||| | | | |||||||| ||||| || |||||||||||||| ||  |||||||||||  
gtaagttactcagttcttgaactctaccaaaacaaatttgacttttgagtgaaatgaaaactgagttttggcttttctttttctgctgtgacagTGACTTGGAATGTAACTTGCACATACTCGCAGTTCTTAGCTCAGAAAACACCAACTTGCTGTGTATCTCTTTCATCGTTTTATAACAAGACAATAGTTTC

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|66918100|gb|CX104948.1|CX104948
EST:     TCCTACTAGGTTCATTTCACTGGATGGCAGAAGAACAACTCAAGCTCATG                         TGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTC
genomic: TCCTACTAGGTTCATTTCACTGGATGGCAGAAGAACAACTCAAGCTCATGgtaagtcatt ... ttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTC
EST: gi|58681522|gb|CK070209.1|CK070209
EST:     TCCTACTAGGTTCATTTCACTGGATGGCAGAAGAACAACTCAAGCTCATG                         TGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTC
genomic: TCCTACTAGGTTCATTTCACTGGATGGCAGAAGAACAACTCAAGCTCATGgtaagtcatt ... ttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTC
EST: gi|58681123|gb|CK069810.1|CK069810
EST:     TCCTACTA-GTTCATTTCACTGGATTGCAGAAGAACAACTCAAGCTCATG                         TGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTC
genomic: TCCTACTAGGTTCATTTCACTGGATGGCAGAAGAACAACTCAAGCTCATGgtaagtcatt ... ttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttttgtctttctggcgtcacaattatgacaccctttcttcctttttttgcagTGACTTGGAATGTGACATGCACATATTCGCAGTTTGTTGCTCAAAGAGCTCCAACTTGTTGTGTTTCACTTTCATCGTTTTACAATGAGACAATAGTTAA
                               caccctttcttccttt  CT-rich tract
                                            ttttttt  TA-rich tract