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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA

Basic information

species Oryza sativa
transcript LOC_Os12g27520.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 6
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcat-cagttgatagctgatgctttctttgc-ttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
||||||||||||||| |||| |||| | |  |    |||||  ||    || || |||| | ||    |   |   |||||   | |||    |   | || | ||  |     |  | ||    ||| || |||| | |  |  || |      |||| | |||||| | ||||| |    |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||
gtgtgtgcacagttctttctattacccctcct---gcacta--taatgcatatacattagttttgtgcattatctgtgctgcattgcagcctgtcattaatccattactcatgcttgtactccagggagtatctaacatc--atgtgat------gtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G179308_T01 (Zea mays), 3'ss of exon 6
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcat-cagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
||||||||||||||| | || |||    |  | | ||  ||||    | |  |   || || ||    ||  |   ||| |   |  ||   ||   | || | |  |     |||| |||  ||||||| |||| | |         | |  ||||||| |||||| | ||||| |    ||||||||||||||||| |||||| | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||
gtgtgtgcacagttcttcctattatcgctcctgc-actataatgcatatacattagtt-tttttttgcaatatatgtgcagcattgtagcctatcattaatccatattactactcatgctta-aggaatatctaacatca--------tgggatgtttatgtatttaccctctctctgtaatgtgttgcagTTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G063792_T07 (Zea mays), 3'ss of exon 4
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
                                                                        ||||  ||||||| | |  ||  || ||||||           | ||    ||| || |||| | |  |  || |      |||| | |||||| | ||||| |    |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||
------------------------------------------------------------------------tgcagcctgtcattaatccattactcatgctt----------gtactccagggagtatctaacatc--atgtgat------gtttttgtatttaccctctctctgtaatgtgttgcagTTATGCATGAATTGCGCCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 5
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
                                                                      |||| |  || |||| | |  |||     | ||     |||||         ||||||| |||| | |         | |  ||||||| |||||| | ||||| |    ||||||||||||||||| |||||| | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||||||
----------------------------------------------------------------------attgtagcctatcattaatccatat----tactactcatgctta--------aggaatatctaacatca--------tgggatgtttatgtatttaccctctctctgtaatgtgttgcagTTATGCACGAATTGTGTCTCATACACACTGATTTAAAGCCTGAGAACATTCTCCTTGTTTCTCCGGAGTACATTAAAGTGCCTGATTACAAA

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
                                                                                        || | |  |  |    |  |||| |     |||| |   ||  ||     | |     |   | ||||  |  | ||   |  | |  |   |   |||||||||||||||| || |||||||| || || ||||| ||||||||||| || ||||| || |||||||| ||  ||||||| || || ||||| 
---------------------------------------------------------------------------------------ctttaaactttgtttactgcttgcattgga-ttttggatttaattagggtttcatt--gtgactctgttgctgaagttgggtggttttgataatactttgcagTTATGCATGATTTACGCCTCATACATACGGATTTGAAGCCTGAGAATATACTTCTAGTGTCTCCAGAATATGTTAAAGTTCCAGACTACAAG

upper sequence: LOC_Os12g27520.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgtgcacagttccttctgttactcttattaccacactaattagcagatctagattattcttccataaattgcatgctgtcatcagttgatagctgatgctttctttgcttcatccttttaggaatacctaatacctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
                                                               |  || || |  |     |    ||||       |||  |||  ||  ||     |  ||   |   |||||    |     |||||      |||| |              |||     ||||||| |||||||| |||| |||||| |||||||| || |||||||||||||| ||| ||||||||||||| ||  | |||||  | || ||||| 
---------------------------------------------------------------tttatgaaataaaaataatatggagtttgagatggataattttgtttatttgctatcctacagagtgctaatgttga-----ctttg---acctataaa--------------aat-----ttgcagTCATGCATGATTTGCACCTCATCCACACTGACTTGAAGCCTGAGAACATACTTTTTGTTTCTCCAGAATATGTAAAAGTATCAGACTACAAG

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|86900381|gb|CI296424.1|CI296424
EST:     AATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCAT                         TTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTC
genomic: AATTGCCCTAGTTCGGGAGGTTGCCAAACAACTGTTGGAATGTATAGCATgtgtgtgcac ... tgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctaacctgctttgtttgtttatatatttatcttctctgtaatgtgtgttgcagTTATGCATGAATTGCGCCTCATTCACACTGATTTAAAGCCTGAGAACATTCTTCTTGTTTCTCCAGAGTACATTAAAGTGCCCGATTACAAA
 acctaac  putative branch site (score: 2)
           tttgtttgtttatata  TA-rich tract