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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag

Basic information

species Oryza sativa
transcript LOC_Os08g42370.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagaca---tgtgcgtatt------------tgtttggagttattcttccagtgc---ttttcatt-----gagctct-------cttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||||| ||||||||||||||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||  |  |   | | ||| ||| |       ||||||   ||| | |  |    |||||  ||             ||||||||| || |||| | | |    ||||||||      || | |       |||   ||    || ||||| ||||| || |||||||| |||||
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaa-catatttg-tgcag

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G068657_T02 (Zea mays), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgttttt-ccagcagttctgtacctatccttaccgta---ggaaagacatgt-gcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
| | ||||| ||||||||||||||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||  ||     || | ||  |||   ||    |||| |   ||   | |  || || | | |    | |||   | ||   ||    ||  | |     | || |||    ||    || || || | ||| ||   |||||| |||||
GTTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttacacaagattactaggtgtttcataggcgtcctcatattacttgaattgatatttagagctactatttctgggtacattttttttgaatgttgactaactttct----attttgttaagactgaccatcaa-tgtatttg-tgcag

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagta-----tcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||| |||| ||||||||||| ||||| || || || || |||||||||||||||||||| ||||||||||| |||||||| || || || || || ||| ||      |  ||| | |  ||   |  | ||    |  || |  |  |   ||    ||    ||||   | ||  | |     |   |  ||  || ||                                                
GCTCTACAGGCCTCCTCGATGCTCGCACTGCTCAATCTGTAATAACTGTGTGGAACGGTTTGACCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTGgtatgttggatcttttgtctcttgagtgttattttattctttttttctttttgtgtgaagaatgt---tttgggggaag--agtagcttaaccccatt-gttaagt-----------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagt---atcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||| |||| ||||||||||| ||||| || || || || |||||||||||||||||||||||||||||||| |||||||| || || || || || ||||||   ||| | | | |||   |||  | |     || ||    |          |||| | |||||   | ||  | | |   | | |    |||| ||        | |                                     
GCTCTACAGGCCTCCTCGATGCTCGCACTGCTCAATCTGTAATAACTGTGTGGAACGGTTTGATCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTGgtaagttggatcttatatctccca-agtgttattttattcttttttctt-------tttgtgtgaatttgggggaag--agtatcttaatcc----cattaagtgtgacagaga-------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA16G26140.2 (Glycine max), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttt-tccagcagttctg-tacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||| |||| |||||||| || ||||| || || || || ||||||||||||||||||||||| || ||||| |||||||| || ||||| || || ||||||   |  |||| |    ||    || |   ||       |  |        || | |     |     ||   | |      ||  | |    |||                                                 
GCTCTACAGGCCTCCTCGATGTTCTCACTGCTCAATTTGTAATAACTGTGTGGAACGGTTTGATCACCATTGTCCCTGGGTTGGGCAGTGCATTGGGCTGgtaagttagaccttttgtttgacaaaattgatttttaattgagtctgatctgcagaatttcctctgctaggcagaaagactggcttggta-tctggggtga-------------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA02G07190.1 (Glycine max), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttt-tccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||| |||| |||||||| || ||||| || || || || ||||||||||||||||||||||| || ||||| |||||||| || ||||| || || ||||||   |  |||| |    ||    ||     ||  |||                || | || || |  |    ||  ||||| ||||   ||   ||       ||    | || | |                           
GCTCTACAGGCCTCCTCGATGTTCTCACTGCTCAATTTGTAATAACTGTGTGGAACGGTTTGATCACCATTGTCCCTGGGTTGGGCAGTGCATTGGGCTGgtaagttagaccttttgtttgacaaaattg-----atttttaat--------------tgtgaatctgctctgcagaat--ttccaatgctaggcagaaagactga--cacggtatctggggt--------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA01G08200.1 (Glycine max), 5'ss of exon 2
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttt-tccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| |||||||| ||||||||||| ||||| || || || || |||||||||||||||||||| ||||||| ||| |||||||| || || || || || ||| ||   || |||| ||    |||  | |   ||| |||           |      |  | ||| |  ||    | |     | | |  ||  || ||                                                
GCTCTACCGGCCTCCTCGATGCTCGCACTGCTCAATCTGTAATAACTGTGTGGAACGGTTTGACCATCACTATCCTTGGGTTGGGCAGTGTATTGGGCTAgtatgttggatcttttgtctcctagtgttat-tttattcttttttcttttttgtgtgaagaatgttt-tgggggaagagtagcttaatcccatt-gttaagtg----------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G38360.1 (Glycine max), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatt-tgtttggagttattc-ttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||| | || |  ||    || || |||||  | ||  | ||||| ||||| || |||||||||||||| ||||||||||| || || || ||||| ||||  | |||  |||      |  |    |  |||  | | |  |||||    ||   |   || | |    ||   |   ||||  | ||     ||||  |                                              
GCTCTACAGACCCCTCCGTGCTTCTCATTGTTCAGTCTGTGATAACTGCGTGGAGCGATTTGATCATCACTGCCCATGGGTTGGTCAGTGTATTGGACTGgtaacaaccattctttc---ataacttcacatttatggt-atccaaggaacactatacacaggttatatacatagccctagattccgatactggcatttgaatt----------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G41060.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||  | || ||||| |||||||| |||||||| |||||||||||||| ||| ||||||| ||||||||||| |||||||| ||||| || |  |  |||||| ||  | |||| | |   | |||| | |    ||           |||||  |  ||| |  ||    | ||||| |  | |  |||    |                                                  
GCTCTATAGACCGCCTCGCTGCTCACATTGTTCGATTTGCAACAACTGTGTAGAAAGGTTTGACCATCACTGTCCTTGGGTTGGTCAATGTATTGCTCAAgtaagtttctcggtttttc-gttttcctgtccgttagtttct---------gacatcagtctatataattcatctcattctccttgggaattt-gcag--------------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G26935.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||| ||  |||| ||||| ||||| || || || || ||||||||||| || ||| ||||||| |||||||| || ||||| |||||||| || ||  | ||||||   |     | | |    | | ||   ||  ||  ||  |  ||  | |  | | ||  | |    |  |  | |||   || || |    |                                                  
GCTCTATAGGCCGCCTCGCTGCTCGCATTGCTCAATTTGCAACAACTGCGTAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATGgtaagtcaaaa----tccaactgatcccgtctttaagctatccacataaaccatagtttcctaaatatc---atctcatattctgatggttgttgcag--------------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagacatgtgcgtatttgtttggagttattcttccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||||||  | || ||||| |||||||||||||| ||||| || ||||| || ||||| |||||||| ||||| || |||||||| || || || ||||| |||||    |  || ||  ||   || || || |||  |    |||      | ||      |  |          |  ||  ||   |  ||||| | |                                                
GCTTTATAGACCTCCTCGCTGCTCACACTGTTCCATATGTAATAACTGCGTCGAACGATTTGATCACCACTGCCCTTGGGTTGGGCAGTGTATTGGACTGgtaagagataaattattttagaccttatg-acatat--tggatgtatagcctatatccaaagaagtaacatttacaaaact--caacaccattcatggggtgggt-------------------------------------------

upper sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv17s0000g00800.t01 (Vitis vinifera), 5'ss of exon 3
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtagg--aaagacatgtgcgtat-ttgtttggagttattctt--ccagtgcttttcattgagctctcttcaaatcaacttgagcctaatcataaagcatatttggtgcag
||||||  | || ||||| || ||||||||||| |||||||| || ||||||||||| ||||| |||||||| || |||||||| ||||| || ||||| ||||  | ||  || ||  | | ||     |    | || |  |||    || | |||   |  ||  ||  |   |  |  ||      ||  | || |||                                                   
GCTTTATAGACCTCCTCGCTGTTCACACTGTTCAATATGCAATAATTGTGTGGAACGATTTGACCATCACTGCCCTTGGGTTGGTCAATGTATTGGACTGgtaatgaaca--ttcttttaactgtatcacatgctttctaaatgtaaattaatgccattgacaaatactgcattatgggaacctagatttgttgtctttatt---------------------------------------------------

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|29656638|gb|CB652913.1|CB652913
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCTCGACCACGTTACTCTGC
EST: gi|88327636|gb|CI646829.1|CI646829
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTT                         CGTAATTATCGGTTCTTCTACATGTTTGTATTCT
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatca ... tttggtgcagCGTAATTATCGGTTCTTCTACATGTTTGTATTCT
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