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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatgctgcctaacaatcacgccatcaggatctgcttatctatcatgtctaatggtctatgctcgcttgaagccattttgttatgatgtttacttaccacgtctagaaatttgttgtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG

Basic information

species Oryza sativa
transcript LOC_Os06g01630.6
intron # 16
splice site 3'
intron type U2

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|25803971|gb|CA759932.1|CA759932
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|88256589|gb|CI358977.1|CI358977
EST:     TATTGGCTCAG                         CTGAGAAGA-GGTGATCCCT-GAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: TATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|88978612|gb|CI384953.1|CI384953
EST:     TCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: TCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|38477221|gb|CF961354.1|CF961354
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|58585940|gb|CF984248.1|CF984248
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|24468761|gb|CA305710.1|CA305710
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|88247217|gb|CI247066.1|CI247066
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|86871900|gb|CI332072.1|CI332072
EST:     CTTTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|89193198|gb|CI050496.1|CI050496
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|86863330|gb|CI344978.1|CI344978
EST:     CTGTGCCATCGTAAATCCTCCACAGTCAGCAATTTTGGCTATTGGATCAA                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCAG
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTC-G
EST: gi|88222196|gb|CI222152.1|CI222152
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|87030828|gb|CI362042.1|CI362042
EST:     ATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: ATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|88257576|gb|CI360162.1|CI360162
EST:     TCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: TCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|86839043|gb|CI330409.1|CI330409
EST:     CCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|88222052|gb|CI222008.1|CI222008
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|86862659|gb|CI345654.1|CI345654
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGGCTGAGGGTCAGTTTGAAGTTGGTTCG
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGA-GCTGAGGGTCAGTTTGAAGTTGGTTCG
EST: gi|89198662|gb|CI016747.1|CI016747
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|86825407|gb|CI360045.1|CI360045
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
EST: gi|86835039|gb|CI346519.1|CI346519
EST:     CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTTAG                         CTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT
genomic: CTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCTCAGgtaacatgct ... gtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccattttgttatgatgtttacttaccacgtctagaaatttgttgtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG
                    tacttac  putative branch site (score: 1)
     ttttgttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatgctgcctaacaatcacgccatcaggatctgcttatctatcatgtctaatggtctatgctcgcttgaagccattttgttatgatgtttacttaccacgtctagaaatttgttgtgtgcacagCTGAGAAGAGGGTGATCCCTGGAGCTGAGGGTCAGTTTGAAGTTGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC