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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaattctcctttgatatttgaataaatatatgtcattgcacaacaaactttcctgatatgcatcttaattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG

Basic information

species Oryza sativa
transcript LOC_Os02g15550.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G060896_T03 (Zea mays), 3'ss of exon 6
gtaacaattctcctttgatatttgaataaatatatgtc--attgcacaa-caaactttcctgatatgcatcttaattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG---------------------------
|||| | || |||||||||   |       |  | ||    ||||  |   | |||||  ||||||  |||| || | ||||||| || ||||||||||||||| | || |||||||||||  |||||||||||||||  |||||||| || ||||                           
gtaa-agttgtcctttgatgccttgcccttttcaagtttagttgcttaggtatactttgttgatatagatctgaactctgtagGTGTGCAAAGATTTCTTCCCACACTTGTCTGTTGGATTTCAAGATCCTCGTGTTCAACTTCATGTCGGCGATGGTATGTAGATAATTCCATGAGGCTATG

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 6
gtaacaattctcctttgatatttgaataaatatatgtc--attgcacaa-caaactttcctgatatgcatcttaattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG
|||| | || |||||||||   |       |  | ||    ||||  |   | |||||  ||||||  |||| || | ||||||| || ||||||||||||||| | || |||||||||||  |||||||||||||||  |||||||| || ||||
gtaa-agttgtcctttgatgccttgcccttttcaagtttagttgcttaggtatactttgttgatatagatctgaactctgtagGTGTGCAAAGATTTCTTCCCACACTTGTCTGTTGGATTTCAAGATCCTCGTGTTCAACTTCATGTCGGCGATG

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120578_T02 (Zea mays), 3'ss of exon 5
gtaacaattctcctttgatatttgaataaatatatgtcattgcacaacaa-actttcctgatatgcatcttaattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG
||||   |||||||||| | | | ||    ||  |||  |  |  |   | ||||  ||||||| ||||||| || | ||| | || || || ||||||||| |||| |||||||||||  |||||||||||||||  |||||||||||||| |
gtaa-ggttctcctttggtgtcttaacct-taagtgtagtcacttagttatacttcgctgatatacatcttatttct-tagATCTGCAAGGAATTCTTCCCACATTTGTCTGTTGGATTTGAAGATCCTCGTGTTCAACTTCATGTTGGTGACG

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|218497061|gb|FG955846.1|FG955846
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|58602035|gb|CK012563.1|CK012563
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|58695758|gb|CK084445.1|CK084445
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|29642051|gb|CB647058.1|CB647058
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|29672898|gb|CB669173.1|CB669173
EST:     GTTCTGTGGAGTCAATTGATATATGTGAGATTGATCAGCTAGTTATTGAT                         GTGTGCAAAGATTTCTTC
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTC
EST: gi|218497953|gb|FG959345.1|FG959345
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|58695993|gb|CK084680.1|CK084680
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|33793719|gb|CF322742.1|CF322742
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|84117386|gb|CD151153.1|CD151153
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|29664250|gb|CB660525.1|CB660525
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|58678117|gb|CK066804.1|CK066804
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
EST: gi|33794317|gb|CF323046.1|CF323046
EST:     GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGAT                         GTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT
genomic: GTTCTGTGGAGTCAATTGATATATGTGAAATTGATCAGCTAGTTATTGATgtaacaattc ... aattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaatatatgtcattgcacaacaaactttcctgatatgcatcttaattatgtagGTTTGTAAAGATTTCTTCCCAGATTTATCTGTTGGATTCAAAGATCCTCGTGTTCGGCTTCATGTTGGTGATG
                                         tcttaat  putative branch site (score: 3)
                                        atcttaattatgta  TA-rich tract