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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_Os01g16900.1
intron # 3
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|29639681|gb|CB644690.1|CB644690
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|58593071|gb|CF991379.1|CF991379
EST:     TGACTATTCGTGAAAATACTGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
EST: gi|29619530|gb|CB624542.1|CB624542
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         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
EST: gi|29664534|gb|CB660809.1|CB660809
EST:     TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAG                         GTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT
genomic: TGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 64 (downstream exon)
Score: 37

TTGCAACAGCCTCCCAGGATACAAGACTCGATATGATGATGTGAACCTTGTGACTATTCGTGAAAATACCGAGGGAGAATATAGTGGCCTTGAGCATCAGgtaagcattc ... tattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttcattggtcttgttagcattattcatcactgtgtgctatttattctccagGTTGTGAGGGGTGTTGTGGAAAGCTTAAAAATTATCACTCGCCAAGCAAGTTTAAGAGTGGCAGAGTATGCTTTCCACTATGCCAAGACCAATGGCCGGG
                                           tttattctcc  CT-rich tract
                                         tatttattct  TA-rich tract