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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_Os04g56970.1
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

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: 71 (upstream exon), 74 (downstream exon)
Score: 5

TCCTTTAATCGGGTCGTCTATTGAGGCGGCTACTGGTGTTGTGTACAATATCACTGGTGGAAAGGACATAACCTTGCAAGAAGTAAACAAAGTCTCTCAGgtgcgtgtaa ... cgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcctaggtgattgaagtgctttgttttgaccaatgcttatgcacgttttgcagATTGTGACAAGCTTGGCCGATCCTTCTGCAAATATAATTTTCGGGGCTGTTGTTGATGACCGGTACACTGGTGAGATTCATGTGACGATCATTGCCACAG
                         ttttgac  putative branch site (score: 5)
                     tttgtttt  TA-rich tract