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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG

Basic information

species Oryza sativa
transcript LOC_Os08g42370.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G821611_T01 (Zea mays), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagaca---tgtgcgtatt------------tgtttggagttattcttccagtgc---ttttcatt-----gagctct-------cttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
||||||  |  |   | | ||| ||| |       ||||||   ||| | |  |    |||||  ||             ||||||||| || |||| | | |    ||||||||      || | |       |||   ||    || ||||| ||||| || |||||||| ||||||||||||||||||||||||| ||||||||||||||||| || || ||||||||||| |||||||| ||||||||||||||  | ||||||||||||  ||
gtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaa-catatttg-tgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G068657_T02 (Zea mays), 3'ss of exon 3
gtaagtatcatgttttt-ccagcagttctgtacctatccttaccgta---ggaaagacatgt-gcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
||||||  ||     || | ||  |||   ||    |||| |   ||   | |  || || | | |    | |||   | ||   ||    ||  | |     | || |||    ||    || || || | ||| ||   |||||| ||||||||||||||||||||||||| |||||||||| |||||| || || |||||||| || |||||||| ||||||||||||||  | ||||||||||||   |
gtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttct----attttgttaagactgaccatcaa-tgtatttg-tgcagCGTAATTATCGGTTCTTCTATATGTTTGTATCCTCGACAACATTGCTCTGCCTGTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCAG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G07190.1 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgct-tttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
                                                ||    || |   | | || || | || | | |||   |  | ||| ||  |  ||  |    |      ||   || |        ||  | |  |||||||||||||||| ||||||| ||||||||| ||||| || ||  |||| ||  | || || || || || |||||||| || || |  |  ||||   | |
------------------------------------------------aattgtatatatatttctggtttg-gtgacttttcagttattattttatacatgtcattcttgaatgttatgtatctgaattgtgcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA01G08200.1 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgt-atttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgag---cctaatca-taaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTT--GCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
                                                     ||| | | | |||| ||| |  || |||    |    ||   ||  |    |||| ||   |  ||  |   ||||||   |    |   |||  |||||||||||||||||||||| | ||||||||| ||||| || ||| || | ||  | ||| | |||  || || || ||||| || ||  | |  ||||      
-----------------------------------------------------cattttcattattttttttgttttgttcagttatcatttgctatgcattattcttgaatatacattatgtatcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTTTTCATGTTTGTCTTCTCAACTACGCTATTGTGTATATACATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGC--

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G26140.2 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgct-tttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttg--gtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
                                                 |    || |   | | || || | || | | |||   |  | ||| ||  |  || ||    |      ||   || |   |   ||| | |||   |||||||||||||||| ||||||| ||||||||| ||||| || ||  |||| ||  | || || || || || |||||||| || || |  |  ||||   | |
-------------------------------------------------attgtatatatatttctggtttg-gtgacttttcagttattatttgatacatgtcactcttgaatgttatgtatctgaatgtgt-gcacaattgttatgcagCGTAATTATCGCTTCTTCTTCATGTTTGTCTTCTCAACTACACTACTTTGTATATATGTTTTCGCATTTTGTTGGGTCTATATTAGAAGAATTATGGAGG

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatca-taaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTA-GAAATG
                                 |||  ||   ||          | ||  || || |  |   | |||      |   | || |||||     | | |  |       | ||||||   |    |   |||  |||||||||||||||||||||||| ||||||||| ||||| || ||| |||| ||  | || || ||||| || || ||||| || ||  | |  |||| |  || 
-------------------------------attattttttttgt----------tctgtttacttttcagttatcatttgctatgcattatt-attgaatatacattatgt-------atcctaattgcttgcacgatttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTGTGTATATATGTTTTTGCATTTTGCTGGGTCTATATTGTAAGAATTATGGCAT-

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTA-GAAATG
                                            | |   | |  | ||  || || |      | |||      ||||  | | ||||     | | |   || | | |       | |  |  || |||  |||||||||||||||||||||||| ||||||||| ||||| || ||| |||| ||  | || || ||||| || || ||||| |||||  | |  |||| |  || 
------------------------------------------aatggaggaaaattctgtttacttttcatctatcatttgctatgtgccatcc-ttgaatatgcattatg-catcctaattg----cttggataattttttatgcagCGTAATTATCGGTTCTTCTTCATGTTTGTCTTCTCAACTACGCTACTATGTATATATGTTTTTGCATTTTGCTGGGTCTACATTGTAAGAATTATGGCAT-

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
                                       |     ||     |  |   |  |  || | ||| | || | |   ||||||    ||| |  |  | |  || ||  ||| |    ||| |    ||  | |||||||||||||||||| || |||| ||||||||| |||||||| ||  | || ||  | || || ||||  ||||| ||||| || || |  | ||| |   || 
---------------------------------------ttttccagttgtcatcttcaccaacatgataggaatgatgcat---gtgcttgaatttgtgggcaatgc--atgaatctgaacactttcaca----attctgggtgcagCGTAATTATCGATTTTTCTTCATGTTTGTCTTCTCGACGACTCTTCTTTGTATATATGTGTTTGGGTTCTGCTGGGTCTATATTAAGAGGATCATGGATT

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|88327636|gb|CI646829.1|CI646829
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCT
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCT
EST: gi|29666673|gb|CB662948.1|CB662948
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|25802931|gb|CA758892.1|CA758892
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACTACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|88301943|gb|CI667789.1|CI667789
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|29672455|gb|CB668730.1|CB668730
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGCCTCTACGTATTTGCTTTCTGTTGGGTGTACATAATCAAGATTAGAAATG
                           gcctaat  putative branch site (score: 3)
                              taatcataaa  TA-rich tract