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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG

Basic information

species Oryza sativa
transcript LOC_Os04g56970.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G119773_T01 (Zea mays), 3'ss of exon 5
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
|||||||||  |||  ||   | |   ||  | ||  | || |          || |   | ||| |    ||||    |||| |  | ||            ||| |          |||    ||   |  |||       || || || |  |     |||||||||| |   ||| ||| | |||||||||||||||||| | || || || ||||| || ||||||||||| || |||||||||||||| |||||||||||||| |||||||| |||||||| ||||
gtgcgtgtaggattcattagaaattcttt--attgattctgca----------atggtgttttaagag---aagttaggaaacgttgggtgtc----------tcaaa----------tagaagaaccaaatatat-------agttgttttagata----gttttgacca-tatgtattcacctcttgcagATTGTGACAAGCCTAGCTGACCCATCTGCGAACATAATTTTCGGTGCCGTTGTTGATGACCGTTACACTGGTGAGATACATGTGACAATCATTGCGACAG

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G02110.1 (Glycine max), 3'ss of exon 5
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatt-tagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
                                                                                         |||| |  ||    |  | ||  |   |  ||    ||||||  | |     ||||  |  |    ||  ||||  ||| ||    |   || |  ||||  || | ||||| || ||||| ||||||||||| ||||| || || || |||||||||||||| || |||||||| |||||||| ||||| || ||||| || |
-----------------------------------------------------------------------------------------tgctgtattccgccttttgctgtatggtggtatacttactgggttcact---cctaccttttcttcgta-tttgccttgtccttaacacgtgtaatttttatagGTGGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGAGCTGTTGTTGATGATCGCTACACTGGGGAGATTCACGTGACTATAATTGCAACTG

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G46530.1 (Glycine max), 3'ss of exon 5
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
                                                                                         |||| |  |     |  | ||  |   | ||    ||||||  | |     ||||  |  |    ||  ||||  ||| ||    |   || |  ||||  || ||||||| || ||||| ||||||||||| ||||| || || |||||||| |||||||| || ||||| || |||||||| ||||| |||||||| || |
--------------------------------------------------------------------------------------ttgtgctgtattttgccttttgctgtatggtata--tttactgggttgact---cctaccttttcttcgta-tttgccttgtccttaacacgtgtaatttttatagGTTGTGACTAGTTTGGCTGATCCTTCTGCTAATATTATATTTGGGGCTGTCGTTGATGATCGCTACACGGGGGAGATTCACGTGACTATCATTGCAACTG

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G10030.1 (Glycine max), 3'ss of exon 6
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaaga-tgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG-
                                                                                 |||||||| |  |||| |||  |  |      ||| || ||   |  |   ||  | ||   | | ||     | |  | |  | |   |||  |||    |  |  || || | |||||||| || ||||| |||||||| ||||| || || || || ||||||||||| || |||| ||| |||||||||||||| |||||||| || | 
--------------------------------------------------------------------------------tacttaagaattttattgtcagaagga------acatttcagcattcttttgatcttatgaatttgttgtgaacatttgtatcctgttttcaaaactt-cataactgctgtaggTGGTGACAAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGTGCCGTTGTTGATGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTGG

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G43500.1 (Glycine max), 3'ss of exon 6
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatca-tactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
                                                                                | ||    ||  ||||  ||  |  |  | | ||  |||       |    |   || ||    |     |||   |    ||||||   |||  |||    |  | ||| || ||||||| || || ||||| |||||||| ||||| || || || || |||||||| || || |||| ||| |||||||||||||| |||||||| || |
------------------------------------------------------------------------------gtacctcggaattttattggcagaaagaacatttcagtattctttttgatcttatgaatttgttgcaaacatttg---tatcctgtttt---caaaactt-cataactgttgtagGTTGTGACTAGTTTAGCCGACCCTTCTGCCAATATTATATTTGGCGCCGTTGTTGACGATCGCTACAATGGGGAGATTCATGTGACTATCATTGCAACTG

upper sequence: LOC_Os04g56970.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv19s0090g01320.t01 (Vitis vinifera), 3'ss of exon 5
gtgcgtgtaatatttcttgccattgtcttgaactgtctttgaagaagtatgatatagcactgtaatatgttaagtcgaaaaacttaagatgctattatcacgatcatactccacaatttagggctactggaattatgtggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
                                                                                    ||      | || |  |    ||  |    ||||      |  |||  || |||   ||       || | |   || |  | |    ||| ||| || | ||  ||| |||| |||||  ||||||||||||| || || ||||| || || |||||||| || ||||| |||| ||| |||||||||||||| || ||||| || |
-----------------------------------------------------------------------------------atagtggctttttttggcacctatcatttgaaattgtccttttgtggggttgtgttttct-------tgcattttcttatgctaatatttgcatatccatgatt--cagGTTGTTACAAGTCTGGCCGATCCTTCAGCTAACATAATATTTGGAGCTGTTGTGGACGACCGCTACAATGGGGAGATTCATGTGACTATAATTGCAACCG

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|25803514|gb|CA759475.1|CA759475
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|88490497|gb|CI427769.1|CI427769
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACCAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|88245610|gb|CI245459.1|CI245459
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCGGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|86423508|gb|CI062269.1|CI062269
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|86425204|gb|CI070301.1|CI070301
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|86505788|gb|CI148421.1|CI148421
EST:     TAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|89179058|gb|CI043563.1|CI043563
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|89195825|gb|CI007244.1|CI007244
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|2311708|gb|C27863.1|C27863
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|88249754|gb|CI249603.1|CI249603
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|88245954|gb|CI245803.1|CI245803
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|8251105|gb|AU091451.1|AU091451
EST:     AGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: AGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
EST: gi|29655651|gb|CB651926.1|CB651926
EST:     TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAG                         ATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT
genomic: TCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
                         ttttgac  putative branch site (score: 3)
                     tttgtttt  TA-rich tract