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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggggctaagggcccagaattttattgtgtatttaaatttctttgcccaaatatctgtattacattcaatttgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g19510.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 10
----------------gtaaggggctaagggcccagaattttattgtgtatttaaatttctttgcccaaatatctgtattacattcaatttgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG
                |||     |          ||  |  |        |     || |||      ||   | ||  |  |  | ||||||||||||||||||||| || |||||||| |||||||| ||  |||||||||||||||| |||||||||||||||
tcgatttatcccttctgtagaccccactcatgtttgacctccaacactaggtcttccttttttttaattatcattctaaaagttcgattttgatgtgcagATTTGTTGAGATTATGGCAACAGTGTTCTCCAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G006507_T03 (Zea mays), 3'ss of exon 10
gtaaggggctaagggcccagaattttattgtgtatttaaatttctttgcccaaatatctgtattaca-ttcaattt-gatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG
             || ||| |  ||| |||||||||||| |||| ||| | || |||   | | | | |||||||| ||||||||||||||||||||| |||||||| |||||||||||  |||||||||||||||| |||||||||||||||
----------gtagggccaaatgtttgttgtgtatttaattttcattgtctaattattattctaaaagttcaattttgatgtgcagATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAG

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G08040.2 (Arabidopsis thaliana), 3'ss of exon 10
gtaaggggctaagggcccagaattttattgtgtattt----------------aaatttctttgcccaaatatctgtattacattcaatttg--atgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG
||| ||  ||     | |    | | ||| | | | |                | | | |||    ||| | ||  ||  |  |    |||   |  ||||| |||||||| || |||||| | || || ||||| || |||||||| ||||| |||||||||||||||
gtacggctctgtactctctttctctcattctctctctttgactaacctactgaagagtgcttatatcaattttcgataacaggtgtgttttcccacttgcagGTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 3'ss of exon 10
---------------------------------------------------------------------------------------------------------------gtaagg--ggctaagggcccagaattttattgtgtatttaaatttctttgcccaaatatctgtattacattcaatttgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG
                                                                                                               ||||    || |||       |  ||      || ||||      || | |||   ||    ||     ||| |  | |  | ||||||||| ||||| |||||  | || |||||| |||| || ||||| ||||| |||||||||||||||
gtatgctttctctctgttctccctctcttgcatatctggtgtgcgtgaatttgtctttatgagtgttaaaacatgcataaacacaatgtaaaaataaatattcaaatatttgtaacatagggtaaatatgttgtcttgggacttgcattttctcccctctcccctcttaggcttacagttttctacatta-attcagATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAG

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|29673249|gb|CB669524.1|CB669524
EST:     GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGC                         ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
genomic: GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGCgtaaggggct ... tgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
EST: gi|29616239|gb|CB621251.1|CB621251
EST:     GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGC                         ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
genomic: GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGCgtaaggggct ... tgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
EST: gi|29676039|gb|CB672314.1|CB672314
EST:     GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGC                         ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
genomic: GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGCgtaaggggct ... tgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
EST: gi|38475807|gb|CF959940.1|CF959940
EST:     GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGC                         ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
genomic: GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGCgtaaggggct ... tgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
EST: gi|33795503|gb|CF323621.1|CF323621
EST:     GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGC                         ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
genomic: GAGGAGAGGCCAGGCTGGTGCACTGATCCCCATCTGCCACCATGTGCAGCgtaaggggct ... tgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT
EST: gi|27577797|gb|CB000492.1|CB000492
EST:     ATCTGCCACCATGTGCAGC                         ATTTGTTGAAATCATGGCCTTCGTGTTCTCTAGGGATGCATGGCGCTGTGT
genomic: ATCTGCCACCATGTGCAGCgtaaggggct ... tgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtatttaaatttctttgcccaaatatctgtattacattcaatttgatgtgcagATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAG
                                          atttgat  putative branch site (score: 5)
                               tattacattcaattt  TA-rich tract