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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcag

Basic information

species Oryza sativa
transcript LOC_Os05g38370.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA11G34120.1 (Glycine max), 5'ss of exon 4
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgt-ctgttgctatttctc--ctatgcgat-gcaaatttgagttcctggtgtctataattgaat-cagctttgtctttgcag-------------------
||||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  ||| || ||   ||  | |   |||  | | | |||  | | |     |     ||  |  ||   | | | |  |    |                    
GTTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGCAGTGCAGGATCTCCTCCAGATATTCCTCCAGAgtactattctcatgccacaattatttgtttggaaacataattatgaagcaaaaatgttcaaaaataacctgggatacaaattctactagtgttctaatta

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA18G04170.1 (Glycine max), 5'ss of exon 4
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgt-ctgtt-----gctatttctcctatgcg---atgcaaatttgagttcctggtgtctataattgaatcagctttgt---ctttgcag-------------
 |||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  ||| |||||     || |||  |  | |  |   |   || | |||         ||  | |  | || | |   |      | | | |             
-TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaaaagttcaaatatcaacctgggatacaaattctactggtgttctaattat

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct------atttctcctatgcgatgcaaa----tttgag------ttcctggtgtctataattgaatcagctttgtctttgcag
||||| |||||||||||||| ||||| ||||||||||| || |||||||| || ||||| || || || || |||||  ||| ||||         | ||||   ||    | |||     | |||       ||  | || | | |||||||      || ||  ||||||
GTTGGAGAAGTTGCAAAAATTACATGTAAGCCAGAATATGCTTACGGAAGAGCCGGGTCTCCTCCCGACATCCCACCTGAgtatgttatgttccaaacttcttgcatctcgttcaagggagtgtgacagttttttttttgtttttgtaattgagatt-tttggtaattgcag

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 5'ss of exon 4
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcag----------------------------
||||| || ||||||||||| || ||||||||||| ||||||||||||  ||| || || || ||||| || ||  |  |||    |  |   | |||| |    ||  | | | ||  |       | | |||| ||| |  | ||| |  | ||                            
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttactatcctgtctcctgtcattgttagaacacaa--gcca-aatttaatta-ttctgtttaagtagaagtaaaacataagatgcccaagcattg

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|25044727|gb|AJ420710.1|AJ420710
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88204275|gb|CI204124.1|CI204124
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88209738|gb|CI209587.1|CI209587
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|14571477|gb|BI118845.1|BI118845
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88836064|gb|CI371169.1|CI371169
EST:     CCAGAATACCCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTA-GAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|38477260|gb|CF961393.1|CF961393
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|58670906|gb|CK059592.1|CK059592
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGG
EST: gi|109711641|gb|CI013246.1|CI013246
EST:     ATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: ATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|58676992|gb|CK065679.1|CK065679
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|86417638|gb|CI031847.1|CI031847
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88980703|gb|CI022414.1|CI022414
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGCCA