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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatattttttttccttaatgagctgaaaattttgtggctgtttagatgtatctactcaacagatttctcatatcttactaatttctttgttgtgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA

Basic information

species Oryza sativa
transcript LOC_Os03g45770.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G814310_T01 (Zea mays), 3'ss of exon 1
-----gtatgatattttttttccttaatgagc-tgaaaattttgtggctgtt-tagatgtatct----actcaacagatttctca--tatcttactaatttctttgttgtgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA
     |    ||||| |||  | ||   |||  |    | ||||||       || ||          | ||| || | ||||    || || ||| |||  |||||| ||||| ||| |||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||| ||||| |||||||||||||||||||| || |||||||| ||||
gtaatgggaaatattctttggcgttttggagtatttgtagtttgtgatgaaaatacattcgctgcagaattcaccaaacttctatattagctcactcattattttgttctgatctttgtagATTATGATTGGGATTCTCTTTTTTCTATTTGAGTTCTATGATGATCAATTGCTTGCGTTTCTTGTTTTGACTCTTGTATGGTTATGCGAGCTATTCACGA

upper sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA15G05080.1 (Glycine max), 3'ss of exon 10
gtatgatattttttttccttaatgagctgaaaattttgtggctgtttagat-gtatc-tactcaacagatttctcat-------atcttactaatttctttgttgt-gatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA
||| |   |  ||||   ||| | |  |         ||  || |||| || || || || |      |||||| ||          || || ||   ||  || | |||   ||||||| |||||||| || || |||||||| |||||||| |||||||||||| | ||||| ||  | || |||| |||||| ||||||||||| || |||||  
gtaagcactcattttaatttatttacttttgtcaaaagtttctatttaaattgtctcgtatttgtgctatttcttattctattagctttgctgatgaattgcttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCCTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC

upper sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 10
gtatgatattttttttccttaatgagctgaaaattttgtggctgtttagatgtatctactcaacagatttctcatatcttactaatttctttgttg----------tgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA
||| |   |  ||||   | | | |  |         ||  || |||| ||              | | | || ||| ||| ||  ||   || |           ||||   ||||||| |||||||| || || |||||||| |||||||| |||||||||||| | ||||| ||  | || |||| |||||| ||||||||||| || |||||  
gtaagcactcattttaattgatttacttttgtcaaaagtttctatttaaattgtctcgtgtttgtgctatttcttattttattagctttgctgataaattgtttattgatttctgcagATTATGATTGGCATTCTGTTTTTTCTCTTTGAGTTTTATGATGATCAGCTACTTGCTTTCATGGTCTTGATTCTTGTCTGGTTGTGTGAACTTTTTACTC

upper sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv12s0034g02140.t01 (Vitis vinifera), 3'ss of exon 10
gtatgatattttttttccttaatgagctgaaaattttgtggctgtttagatgt-atctactcaacagatttctcatatcttactaatttctttgttgtgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA
    || ||| || | ||||  ||   |     ||||||  ||  ||  || | |||  |       ||  ||  |   | |  || || | |||||   ||  |||||||||||||||| ||| | |||||||| ||||| || |||||||||||  |  | |||||  | || || | |||||| |||||||| |||||||||||  
---cga-attgttgtgcctttctgttttt---tttttgtttctccttgtatattatcctccatgattatcactgttgattgataaaattgtgtgttgcattc--tgcagATAATGATTGGTATCTTATTTTTTCTCTTTGAATTTTATGATGATCAACTATTGGCATTCATGGTCTTAATTCTTGTCTGGTTGTGCGAGCTATTTACAC

upper sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S96_202V6.1 (Physcomitrella patens), 3'ss of exon 11
gtatgatattttttttccttaatgagctgaaaattttgtggctgtttagatgtatctactcaacagatttctcatatcttactaatttctttgttgtgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA
 |  ||     |  ||  |  ||| |  |  | | |||||| |    |  | | | |  | |  |||  | | |  | ||  |     ||  ||||||||    |||||||||||||||||| |||||||| || || ||||| |  ||||| ||| ||||||| ||||| ||  | || || || ||| | || ||||| || || |
-tgggagtggctgattagtagatgcgtggtgagtcttgtggattgacatgtttttgtgttaactagaccttttagctgttgttg---cctcggttgtgat----gcagATAATGATTGGGATACTCTTTTTCCTGTTCGAGTTTTTCGATGACCAGCTGCTTGCGTTTCTGGTCCTCACACTGGTCTGGCTTTGCGAGCTCTTCACTA

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|58695202|gb|CK083889.1|CK083889
EST:     CATTTCAACTGATATTTGTCCATGTTATCGAATCATTGGTTTTTGTTCCG                         ATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTG
genomic: CATTTCAACTGATATTTGTCCATGTTATCGAATCATTGGTTTTTGTTCCGgtatgatatt ... atcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTG
EST: gi|218491801|gb|FG954125.1|FG954125
EST:     CATTTCAACTGATATTTGTCCATGTTATCGAATCATTGGTTTTTGTTCCG                         ATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTG
genomic: CATTTCAACTGATATTTGTCCATGTTATCGAATCATTGGTTTTTGTTCCGgtatgatatt ... atcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctactcaacagatttctcatatcttactaatttctttgttgtgatcattgcagATAATGATTGGGATCCTCTTTTTTCTATTTGAGTTCTATGATGATCAGTTGCTTGCATTTCTAGTTTTGACTCTTGTATGGTTGTGTGAGCTATTTACGA
                          tactaat  putative branch site (score: 1)
                    atatcttactaattt  TA-rich tract