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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G39540.1 (Glycine max), 3'ss of exon 5
gtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataatt--ttctaaaactgaacc--agGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA
                                                                       |       |   | |||  ||  |||||  | |   |  ||  |||||  ||| |  |||  ||  |||  ||   |  || |     ||||  |  | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  |  |||| |||| |||||| ||||| || |||||||
----------------------------------------------------------------------gtgaatgctagattgtagt-ttcatggttg-attattattttattttttacaaagtatcatgtaaccattggtttacatgctcatttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATA

upper sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 5
gtgagtcattatgatctcaacaagcaccgtccttctgattttaactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggttacacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA
                                                                      | ||| | | ||   |  |||   || | |   || ||  ||  |       | | || |   | |  ||| |     ||     ||||  |  | ||||| ||||||||||| |||||||||||||||  ||| ||||||||||| ||  | ||||| |||| |||||| ||||| || |||||||
-------------------------------------------------------------------gtgaatgctagattgtagtttcatggctgatcattatttcat-tttttacaaagtatcatgtaaccattggtttacatgttcttttttagGGCTCCAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATA

upper sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------gtgagtcattatgatctcaa--caagcaccgtccttctgatttt----aactactaacaggcagatcttgtcacacattgccataatgatatagcatttgtggtta--cacttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA
                                    || |  || | | |  |     |  | |  |  ||| || ||||    ||    |       | ||||  ||| | |||  || |   ||      ||     ||    |   |  ||||    |||||    ||   ||||||  || | |||  ||| | |||||  |  |  ||||  | |||||||| |||||||||||||||  ||| ||||||||||||||  | |||| |||||||||||| || ||  | ||||| |
gtgagttgtccaaattctaaattaagtttgaacattgtcatgcactcttaattttgttcttggattggacttatgtttttctaaaatgttttgtgaaaacatctactca-agattttcaaatccattctttcttaacatttggttatccattgattttccttttt---ttttttttaaatt-ttctttaatgctgtaacagGGATCTTGTGTTGGCCTATATTTTATCAACAGACCTGAGTGGCTCATTGTTGATCATGCCTGCTCTGCATTTTCATATGTATCAGTTCCTTTATATGACA

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|33675569|gb|CF303808.1|CF303808
EST:     CAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAA                         GGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTT
genomic: CAAGCCGGACTGCGATAGGTTCTGGTCTTATTTACCATGGAATACCTGAAgtgagtcatt ... actgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttacagattcctttttttaaacttgcattaaataattttctaaaactgaaccagGGTGCGCGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGACCATAGTTGATCATGCCTGTGCGGCATATTCATATGTATCCGTGCCACTTTATGATA
                                      ttctaaa  putative branch site (score: 2)
            tttttttaaacttgca  TA-rich tract