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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG

Basic information

species Oryza sativa
transcript LOC_Os09g21770.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G091265_T05 (Zea mays), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggt-ttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
      |  | || | |  |   || | | | | ||  |  ||     | |  |   | || | | |    |||| || |  || ||||     ||||   ||||| | ||  |||    ||| ||| |||| || || |||||||| ||||||||||| ||||||||||| || ||||||||||| || ||||||||||||||
------gtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattat---ttttgcttctgatg-taat-----gtgggatttttgatcttatgtgacattgtttgtatgtgaagATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G091265_T01 (Zea mays), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggt-ttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
     ||  | || | |  |   || | | | | ||  |  ||     | |  |   | || | | |    |||| || |  || ||||     ||||   ||||| | ||  |||    ||| ||| |||| || || |||||||| ||||||||||| ||||||||||| || ||||||||||| || ||||||||||||||
----gtgtacaaagctcttccttttctgtaaccttttgtcatgtggtggttaatcagtttgtattat---ttttgcttctgatg-taat-----gtgggatttttgatcttatgtgacattgtttgtatgtgaagatattgcaagTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G35680.2 (Glycine max), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttt-tggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                                   | | |||   |||| || || |  ||  ||       |||   ||  |   |||||| |||  || ||| | | || |||  |  | |||| || || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||
----------------------------------gtaagtttatttctgttttttttagtgagat---aatgttgtaagtgtttgaaatggtgggttttgttttgttgatttggttcggttttgtg-gtttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G34740.3 (Glycine max), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttt-tggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG-------------------------------
                       |||||| ||   || ||||    |||    |  |  ||   | || | |||   |||  ||| |||||| |||  || ||| | | ||  || ||  | ||||| | || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||                               
------------------gtaagtttttttatttctgttttta---ctgag-ataatggtgttgtttgtgttttaagtgt-ttga-aatggtgggttttgttttgttgatttagtttggttttgtgt-tttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGGTAAAACCAGTATATTCTGCTTTTTTTTGTT

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                             | | ||||||| ||     | | |   || ||   | | ||   || | |  ||  |  |  ||  |  |  ||    |||   |||| || ||||| | || ||||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||
---------------------------gaggttattgattgtggg---gatggggattttg-ggttttggaactgatggggcttttctttttttcttttc-ttgaactttttttgtg-gtttgtgt-tttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G34740.1 (Glycine max), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttt-tggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                       |||||| ||   || ||||    |||    |  |  ||   | || | |||   |||  ||| |||||| |||  || ||| | | ||  || ||  | ||||| | || ||||| ||||||||||||||||| |||||||| ||||| || ||||||||||| ||||| |||||||| ||
------------------gtaagtttttttatttctgttttta---ctgag-ataatggtgttgtttgtgttttaagtgt-ttga-aatggtgggttttgttttgttgatttagtttggttttgtgt-tttgaagGTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgt-gcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                                 |  | ||||   | || ||   |    | |  | |  | ||  || |  |  |   ||  || || ||    ||   || | | |  || ||||| | | ||||| ||||| || |||||||| ||||||||||||||||| ||||| || || || || |||||||| ||
-------------------------------ggaggggtttt---tttggtttcaggcccg-agggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                                   ||| ||||  |    ||| ||   ||     ||    |||  ||||||| || | || ||  |  |  |   ||||  |     | ||| |   || ||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||||||||| |||||||||||
----------------------------------gtgagtttgagttgttttgctggattgatgattgatgattgaatgtactggtattcgtgggctgatgaatacttttgaat-----tttgtat---tgaagGTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv12s0059g01180.t01 (Vitis vinifera), 3'ss of exon 2
---------------gtatttgctccaaccccccctccttttttgat-cattgattttgcatctgcttgttg--ttatgcaatgtgggctttggttgtactgataat----ggttggtggtggttttggtttgggtgtgtgtgtgtgt--gtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                |    | |  |||  |   |   |  | ||  ||   | ||    ||   |||||    ||   | |    |  |||| |||  |||   |    | ||||   ||  |   | |||  ||| | || || |   | |  ||||| || |||||||||||||| ||||| ||||| || || |||||||||||||| ||||||||||||||
gtgagtccgagttccattaaagattaaactgcatttagctcatagaagcagaaaattactttcaaattgttaaactaataattacttggattggatgttttgagggtttttgattggcactgactgatgcttgaatgtttttgggttttgatttaaagGTATTGTAAGTGCGAGATGCCTTATAATCCGGACGACCTTATGGTGCAGTGCGAAGGATGCAAGGACTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ05369 (Selaginella moellendorffii), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                                                            | ||  | | |   | |   |||    ||  |   |     || || | |   | | || || || |    |||||||||||||||||||||||| || |||||||||||||| ||||||||||| ||||  ||||| |||||
------------------------------------------------------------gtaagattgacaaagctctcactttggattctctatc----ttatgctctctttttttgggtttgcggaaacagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

upper sequence: LOC_Os09g21770.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ26805 (Selaginella moellendorffii), 3'ss of exon 2
gtatttgctccaaccccccctccttttttgatcattgattttgcatctgcttgttgttatgcaatgtgggctttggttgtactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
                                                            | ||  | | |   | |   |||    ||  |   |     || || | |   | | || || ||      |||||||||||||||||||||||| || |||||||||||||| ||||||||||| ||||  ||||| |||||
------------------------------------------------------------gtaagattgacaaagctctcactttggattctctatc----ttatgctctctttttttgggtttgaa---acagGTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTG

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|33663380|gb|CF294347.1|CF294347
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatttgctc ... gtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
EST: gi|29638119|gb|CB643128.1|CB643128
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatttgctc ... gtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
EST: gi|29638253|gb|CB643262.1|CB643262
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatttgctc ... gtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
EST: gi|86851116|gb|CI311334.1|CI311334
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         GTACTGCAAGTGCGAG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatttgctc ... gtgtgtgcagGTACTGCAAGTGCGAG
EST: gi|29638118|gb|CB643127.1|CB643127
EST:     TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGT                         GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG
genomic: TTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatttgctc ... gtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTG

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: 70 (upstream exon), 69 (downstream exon)
Score: 14

AGAACTACACCAAGCTCGACAACGTCGGCCCCGAGGACTTCTTCTGCCGCTTCGAGTACAAGGCCGCCACCGGCGCCTTCACCCCCGACCGCGTCGCCGTgtatttgctc ... gtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgataatggttggtggtggttttggtttgggtgtgtgtgtgtgtgtgtgcagGTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTG
 tactgat  putative branch site (score: 14)
     ataat  TA-rich tract