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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG

Basic information

species Oryza sativa
transcript LOC_Os07g47290.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G313536_T01 (Zea mays), 3'ss of exon 4
gtatggctattacctggtttcatgtttaggttcagttc-----------attatgaatttgcacgtttgcttaatcaac-aacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||  |||    |    ||  | || ||| |            |||||  || |   ||||| |  |  ||| ||||||||| | || ||  ||| |||||||||||||||||||||||||||||||| | |||||  |||  ||||||||||||||||||||||||||||| ||||| || |||||    
gtatgatgatcgcctaacctacctttgtgctttagtcctagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactgacatttcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTCAACAAATGGTGCTTCCATGACAGGGATATTGCCCCGGATGGGAAGACACTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G005493_T01 (Zea mays), 3'ss of exon 5
gtatggctattacctggtttcatgtttaggttcagttca----ttatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   || ||||    | |   |  | |  |||||     || ||  ||   | ||||| |  |  |  ||||||||| | |||   ||||||||||||||||||||||||||||||||||||||| || |||||||  |||||||||||||| |||||||||||||||||||| ||||| |||   
gtatgaggatcacctaacctaactctatgttgtagttccagccttctgggtt---atgtttgttgga--actaacttctgtttcaatcactattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTGGGGGTTGACAAATGGTGCTTCCATGATAGGGATATTGCCCCTGATGGGAAAACTCTCGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G335948_T01 (Zea mays), 3'ss of exon 3
gtatggctattacctggt-----ttcatg-tttaggttcagttc-----attatgaatttgcacgtttgcttaatcaac-aacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||  |||        ||  || |||||   |||         |||||  || |   ||||| |  |  ||| ||||||||| | || ||  |||||||||||||||||||||||||||||||||||| | |||||  |||  |||||||||||||| |||||||||||||| ||||| || |||||    
gtatgatgatcgcctaacctacctttgtgctttagtcccagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactgacattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTCAACAAATGGTGCTTCCATGATAGGGATATTGCCCCGGATGGGAAGACACTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081682_T02 (Zea mays), 3'ss of exon 5
gtatggctattacctggt-----ttcatgtt-taggttcagttc-----attatgaatttgcacgtttgcttaatcaac-aacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||| |||        ||  || | |||   |||         |||||  || |   ||||| |  |  ||| ||||||||| | || ||  |||||||||||||||||||||||||||||||||||| | ||||||||||  ||||||||||||||||||||||||||||| ||||| || || ||    
gtatgatgattgcctaacctacctttgtgctgtagtcccagccttctgggttatgttttggtctgtttgttggaagaactaacttctgtttcaactggcattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTTGACAAATGGTGCTTCCATGACAGGGATATTGCCCCGGATGGGAAGACTCTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC190975.3_FGT004 (Zea mays), 3'ss of exon 2
gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   ||  |||    |    ||  | |  ||| |      |   | |  | ||   |  |        ||||| | |||||  |||||||||||||||||||||||||||||||||||| | ||||| ||||  ||||||||||||||||||||||||||||| ||||| || |||||    
gtatgatgatcgcctaacctacctttgtgttgtagtccc-----agccttctgggttatgttttgg------tctgtttcaattggcattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGTTGGGAGTCGACAAATGGTGCTTCCATGACAGGGATATTGCCCCGGATGGGAAGACACTTGAA

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 5
gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
|||||   |||      | ||  ||| |  | |    ||||  ||  ||    |||||  | |  ||  |    | ||| ||||   ||  ||||||||||| |||||||||||||    || || || ||||||   ||||| ||||| ||||||||||| ||||||||||| ||||| ||   |
gtatgttaattcttgactctccagttgatatacttcacattcagatatt---tgtttgtgtcacaaaataaaattctcttaatt---atcacagTGAGAGCTAACTTTGAGTTCATAAGCAAACTCGGTGTTGACTTTTGGTGTTTCCACGACAGGGATATAGCCCCTGATGGAAAAACTCTTGAG

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G57655.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
||| | | |     || ||| ||||| || |||  ||| ||||  | || |  ||    | | | |   | |  ||| | |        ||||||||||||| ||||||||||| || |||| |||||||||||  ||||||| || |||||||| || || || ||||||||||  |||||   |
gtaagtccagattgtgtttttatgtt-agtttctcttcgttatcgagttac-tgtgatttgagttactgattgttgtttaa--------tgcagTGAGAGCTAACTTTGAGTTCTTGAAGAAACTTGGAGTTGATTGGTGGTGTTTTCATGACAGAGACATAGCACCTGATGGCACTACACTTGAG

upper sequence: LOC_Os07g47290.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 6
gtatggctattacctggtttcatgtttaggttcagttcattatgaatttgcacgt------ttgcttaatcaacaacttctgtctg--aattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
         | |  ||  |  || ||    |||  || ||||    || | |  |      |  | | | | |    ||   |||   || |   | |  |||||||||  ||||||||||||| || ||||||||||| ||    ||||||||||||||||||||||| ||||||||||| ||||| ||   |
--------gtaagttgaatctatattgttcttccatttattaattgttggaaaatagtgtataacatgaccgatctttttcctctattaaatacaact-tagTGAGAGCCAACTTTGAGTTCATTGAAAAGCTTGGAGTCGATCTATGGTGCTTCCATGACAGGGATATAGCCCCTGATGGTAAAACCCTGGAG

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|29625366|gb|CB630377.1|CB630377
EST:     TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT
genomic: TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAAgtatggctat ... gttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT
EST: gi|29637953|gb|CB642962.1|CB642962
EST:     TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAA                         TGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT
genomic: TTGGCCTTGGGAGGATGGCACAAATTCGTTGGACATGGCTAAGAGAAGAAgtatggctat ... gttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgaatttgcacgtttgcttaatcaacaacttctgtctgaattgttattgcagTGAGAGCTCACTTTGAGTTCATGGAGAAGCTTGGAGTTGACAGGTGGTGCTTCCATGACAGGGATATTGCCCCTGATGGCAAAACACTCACG
                  gcttaat  putative branch site (score: 4)
                                         aattgttatt  TA-rich tract