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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

Basic information

species Oryza sativa
transcript LOC_Os12g27520.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 4
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
              | | ||| | | |||  |||           | |||| || |||||| || | |  || ||||||||||||||  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-------------gtgagtttgctggttcagttagc---------acctatatgcgtgctt-acgttcataagattgcttgtatata--agctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
              | | ||| | | |||  ||||          | |  ||||| |||||||| | |  || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-------------gtgagtttgctggttcggttaac---------acccttctgtatgctttacattcataagattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 3
gtgagtcctatggttcacttttccgtttcccttaagtaactgt-tgatctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||   |   || ||||     | || | || |  | |   |  |  |        | ||  || |     |||| ||    | ||  |||  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagt---agatttaacttaaatttgtcacgtatgctagtacatactacaatgaaaatccttgattccattgcattggtt----aaatgggcttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgat-ctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||  |    || || |     ||| | |    ||  ||    | | |  |     ||||  || |     |||| ||    | ||  | |  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtatt----tttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggtt----aaatgggtttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgc-ttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||  | ||         |    || | |    ||  ||    | |       | |  || |||      ||||| |||  || ||  | |  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtattttgacctgaaacttttcttacatgttatatatgccagtatg---acataccatatttg-attccattgcattggttaaatgggtttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 3
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||  | |   | ||||     | || | || | |       ||  |  |   || ||   ||||          |||  || ||  |||  |     |||||||||||| ||||| ||||||||||||||||||||||| ||||||||||||
gtaagtaattt---taacttaaatttgtcacgtatgcatactacaatgaaaatccttgattccattgca---------ttggttaaatgggcttatt--ccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtcctatg-gttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttacttgcgcaatattgcttgtatatat-aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| ||| || |  ||| |||||| | |    | | | |||    ||||  |     |     |  |     | | ||  ||| | |  | ||     | ||||  |||||||||||| ||||||||||||||||||||||||||||||||||||||||||
gtaagtactgtctgttgactttttcttcatgcatcactaatc--tgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttactt-gcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
||||||  |         | ||   |         |  |||||||       | |  ||||| ||  ||    | |   | || || || || |  |    ||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggt-taaatgagtttatt--ctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 4
------gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctat--ctgtgtgctttacttg---cgcaatattgcttgtatatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
      ||   | |  |        |  | ||      |  ||| ||| |  |   |  |  | || |    |||    | ||| | | |||  |   ||||   || ||||  ||||||||| | |||||| ||||||||||||||||||||||||||||| ||||||
gtaagtgtagtttccttctacttgatcactgtcatttgttggtatctgctattaggttgccctttggtcagtttgaggtgaaatttgggttg-gtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT

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|29665166|gb|CB661441.1|CB661441
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGAAAAAAGTAGATCCAG                         TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGAAAAAAGTAGATCCAGgtgagtccta ... tattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|29668017|gb|CB664292.1|CB664292
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGAAAAAAGTAGATCCAG                         TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGAAAAAAGTAGATCCAGgtgagtccta ... tattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|29689119|gb|CB685394.1|CB685394
EST:     GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGAAAAAAGTAGATCCAG                         TTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGGCATGCTCGAGCAGCTTGGTAAATATGAAAAAAGTAGATCCAGgtgagtccta ... tattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgctttacttgcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT
                                           tctatttt  CT-rich tract
                          ttgtatatataa  TA-rich tract