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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG

Basic information

species Oryza sativa
transcript LOC_Os01g16900.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 3
gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
||||||||||||||| |  || |   ||  |||  | |    |  ||| ||  ||||  |||  || ||   || ||||||||||| |||||||||||||| || |||||||| || |||||||||||||| ||||||||||||||||||||||| ||||||||| ||||||||||||
gtaagcattcttaaa-gagatgttgcttcaattattgtcaccatgattctttttcaccttgtcttaattccacttcagGTTGTGAGAGGTGTTGTGGAAAGTTTGAAAATTATTACACGCCAAGCAAGTTTGAGAGTGGCAGAGTATGCTTTCCATTATGCCAAGGCCAATGGCCGGG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 3
gtaagcattcttaaaagcaatatcattttcattggt-----cttgttagcattattcat---cactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
||||||||||||||| |  || |   ||  |||  |      |||| ||||| |||| |   |||  ||| ||| ||   |||||||||||||| |||||||| ||||| || |||||||| || |||||||||||||| ||||||||||| |||||||| || ||||||||| ||||||||||||
gtaagcattcttaaa-gagatgttgcttcaattattgtcagtttgtcagcatgattctttttcaccctgtcctagtttcgctccagGTTGTGAGAGGTGTTGTAGAAAGTTTGAAAATTATTACCCGCCAAGCAAGTTTGAGAGTGGCAGAATATGCTTTTCATTATGCCAAGGCCAATGGCCGGG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G06590.2 (Glycine max), 3'ss of exon 2
gtaagcattcttaaaagcaatatcattttc-attggtcttgttagcattattcatcactgtgtgctatttatt--ctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
||||   |    | ||   || | |  | | ||   | |  ||   || | |      ||| |   ||||||      ||||||||||| |||||||| |||||  | ||||| || || || |||||||||||||| || || ||||||||||| |||||||||||| |  ||||  | |
gtaaatttcacaacaattgatgttacatactatcattttaattctgatcaatataatttgtttagcatttatgggtctcagGTTGTGAGAGGTGTTGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 2
gtaagcattcttaaaagcaatat---cattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
||||   |    | ||   ||      | | ||||  |  || | | || |||   |   |  |   | |||    | ||||||||||| ||||| || |||||  | ||||| || || || |||||||||||||| || || ||||||||||| |||||||||||| |  ||||  | |
gtaaatttcacaacaatttatgcacgtactatcatctgaattctgatcaatataatttgtttagcatt-tttgggtttcagGTTGTGAGAGGTGTAGTAGAAAGTCTCAAAATCATTACACGTCAAGCAAGTTTAAGGGTAGCTGAGTATGCTTTTCACTATGCCAAGGCTCATGGAAGAG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G03290.1 (Arabidopsis thaliana), 3'ss of exon 2
------------gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctattt---------attctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
             ||||  |  | |      || |||  ||  ||  |||  | |    |  | || |  || |  | ||          ||     ||||||| || ||||| ||||||||  | ||||| || || || || || ||||| ||||| |||||||||||||| | ||||||||||||  ||||  | |
gtttagtttgttttaagtctattgatcgaatatttcaggttagttcttctaataaatgattctaatgatggttttgttttctcctgacgcatataatagGTTGTTAGAGGTGTGGTGGAAAGTCTTAAAATCATTACCCGTCAGGCGAGTTTGAGAGTTGCAGAGTATGCTTTTCTCTATGCCAAGACTCATGGAAGAG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 2
gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattct--------ccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
|| ||   | || ||    || | ||  ||||  | |   |    | |    |  | | ||    |||| || |        |||||| ||| | ||||| || |||||| | ||||| || ||||| || || ||||| || ||||| |||||||| || ||||||||||||||| ||||  | |
gtgagttgttttcaagaggatttaatgctcatctgacaaatacttaatgcatagaaatttgaaggatttcttgtaattggtgccagGTGGTGCGAGGTGTAGTTGAAAGCCTCAAAATAATTACTCGTCAGGCTAGTTTGAGGGTGGCTGAGTATGCATTTCACTATGCCAAGACCCATGGAAGAG

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ18109 (Selaginella moellendorffii), 3'ss of exon 3
gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
              ||||||        |   |||| ||   ||  |   || |  ||||  |   ||  || | ||||| ||||  ||||||||||| ||| | || ||||||||||||||||| ||| |  | || || |||||||| |||||||| ||||| ||||| ||  |  
------------gtaagcaaag-----cttgctggtttt-cgagtttcgatcttggctgttgg---ttccttttgcagGTGGTGAAAGGTGTTGTGGAGAGCCTTAAGATTATCACTCGCCAAGCTAGTATGCGTGTCGCGGAGTATGCGTTCCACTACGCCAAAACCAACGGTAGAA

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ09610 (Selaginella moellendorffii), 3'ss of exon 2
gtaagcattcttaaaagcaatatcattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
              ||||||        |   |||| ||   ||  |   || |  ||||  |   ||| ||   ||||| ||||  ||||||||||| ||| | || ||||||||||||||||| ||| |  | || || |||||||| |||||||| ||||| ||||| ||  |  
------------gtaagcaaag-----cttgctggtttt-cgagtctcgatcttggctgttgg---tttctttcacagGTGGTGAAAGGTGTTGTGGAGAGCCTTAAGATTATCACTCGCCAAGCTAGTATGCGTGTCGCGGAGTATGCGTTCCACTACGCCAAAACCAACGGTAGAA

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|163928585|gb|EG710882.1|EG710882
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|14571344|gb|BI118712.1|BI118712
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58593071|gb|CF991379.1|CF991379
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58669476|gb|CK058162.1|CK058162
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58691994|gb|CK080681.1|CK080681
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|66923182|gb|CX110030.1|CX110030
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
                                           tttattctcc  CT-rich tract
                                         tatttattct  TA-rich tract