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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA

Basic information

species Oryza sativa
transcript LOC_Os01g54080.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G323622_T01 (Zea mays), 3'ss of exon 4
gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
|||||| |||   |    |    |  |||  || |   |||| ||     || | ||||| ||| ||||| |  |||| ||   ||| |  ||| |||||| ||||| |||||||| ||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || ||
gtatatcttaagtatgttaatggtgcaatctaaaatttaaaagtt----gtataattgaatattactcaccaagttttcttgcctaatttccagTTGAAGTATTCTCTGATATCCAGCCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGTTCAGGAAAGACTTA

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G124883_T01 (Zea mays), 3'ss of exon 4
gtatatattagtaa--gagcaggaatttaattaaagaaaaaaaaatttggca----tacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
|||||| |||       || | |   |||||     ||   |||||||   |    ||   ||| | |||||||||||  |||| ||   ||| |  ||||||| || ||||| |||||||||||| |||| ||||||||||||||||| || ||||| ||||||||||| ||||| |||||||| || ||||| || ||
gtatatcttaactcttaagtatgttattaatggtctaatctaaaatttaaaagttgtatcattggatattgctcacaaagttttcttacctaatttccagCTGAGGTATTCTCTGATATCCAACCTCTGATCAGATCAGTTCTTGATGGGTTTAATGTGTGCATTTTTGCCTATGGTCAAACTGGATCCGGAAAGACTTA

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G04580.1 (Glycine max), 3'ss of exon 5
--------gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
        | ||  |||  |   | ||    ||   |    ||  ||    ||  |   ||| |  ||  |||  |  | | | |||  |   |     |||| || || | ||| || || ||| | || || ||||||||||| |||||||  ||||| || || ||||| ||||| |||||||||||||| ||||| ||
aggttttaggattaattttttttatcacagtttc--tccctgattaagttgttatgttaacattctaatgttgtactaatgatattaaattgaataatgcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGATATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 13
-----------------------------gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatt-tggcatacagttgaacattgctcacaagcttttat-ttgataactcac-----agCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
                              |   ||||| ||  |  |  | | | ||||  |  |      || |    |  |  |  | | |  |    | ||| ||| |  |||  |  |     ||  ||| | |||   || |  ||||| |||||| |||| ||||||||||| | ||||||||| || ||||| ||||| |||||||| || ||||| |||||
gtactgcgtttttttttcttttctctttcatgattattattattattattattattattattggtacttgttttctattgttgaaattgatagtaatgtttaacttatatgtcaatatttttctttgtagAGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACTGGCTCGGGAAAGACATA

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 13
-------------------------gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
                          |  ||  |  | |      | | ||  ||          |||||     ||  ||| ||| ||   ||  |   ||| | |      |   ||  ||| | |||   || |  ||||| |||||| |||| ||||||||||| | ||||||||| || ||||| ||||| ||||| || || ||||| |||||
gtactgcatttttttttcttttctatttcatgattattattattagtacttgttttctattgttgaaattgatagtaatgttcaac-ttatacatcaatatttttct------ttgtagGGGAAATATTCAAGGACACTCAACCATTGATTCGATCTGTTCTTGATGGGTACAATGTTTGTATATTTGCTTATGGTCAAACCGGCTCGGGAAAGACATA

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA05G35130.1 (Glycine max), 3'ss of exon 11
-------gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
       |  ||  ||  | |   |||    |   ||    |      |  ||  | | |   ||     | || |  |  ||  |||  ||||    |||| || || | ||| || || ||| | || || ||||||||||| ||||| |  ||||| || || ||||| ||||| |||||||||||||| ||||| ||
gttttaagattaatttttttaacacagtttctcccttttttagttgttatgttaaccttctaatg--ttgtactaatgatattaaattgaataat--gcagCGGAGGTATACTCTGACATTCAATCCTTTATAAGATCAGTTCTAGATGGGTATAATGTGTGTATATTTGCTTATGGCCAAACTGGTTCAGGGAAAACTTA

upper sequence: LOC_Os01g54080.1 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ30678 (Selaginella moellendorffii), 3'ss of exon 9
gtatatattagtaagagcaggaatttaattaaagaaaaaaaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
                                        |  ||    ||   | |   || |  ||||||  |   |  ||    |   |||  || |||||    |||   || ||||||||| |||| || |||||||| ||||| || || |||||||| |||||||| |||||||| |||||||||||
--------------------------------------gtacgttctatattttgctc--caatagtcacaa--tgacacgtg----catgcagACGAGGTTTTTCTGGATGCGCAGCCTTTGATTCGATCGGTGCTTGATGGTTTCAACGTCTGTATTTTTGCGTATGGACAGACTGGTTCTGGAAAAACATA

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|58683961|gb|CK072648.1|CK072648
EST:     TATCGAATGTTTAAGTTTAACAAAGTGTGCGGTACACATTCGCTCTCAAG                         CTGAAGTTTGG-CCGATATCCAACCTTTGATTAGATCAGTTCTGGATGGA
genomic: TATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTC-CTCTCAAGgtatatatta ... taactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGA
EST: gi|66917351|gb|CX104199.1|CX104199
EST:     GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAG                         CTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT
genomic: GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAGgtatatatta ... taactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT
EST: gi|58684417|gb|CK073104.1|CK073104
EST:     GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAG                         CTGAAGTTTTCTCCGATATCCAACCTTTGATCAGATCAGTTCTTGATGGAT
genomic: GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAGgtatatatta ... taactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT
EST: gi|58677888|gb|CK066575.1|CK066575
EST:     GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAG                         CTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT
genomic: GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAGgtatatatta ... taactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT
EST: gi|33675793|gb|CF304032.1|CF304032
EST:     GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAG                         CTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT
genomic: GTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAGgtatatatta ... taactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGAT

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), 43 (downstream exon)
Score: 11

GAAAATGGCGAGATTCTTATTGCAAACCCCTCCAAGCAAGGAAAGGAAGGGTATCGAATGTTTAAGTTTAACAAAGTGTTCGGTACACATTCCTCTCAAGgtatatatta ... taactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatttggcatacagttgaacattgctcacaagcttttatttgataactcacagCTGAAGTTTTCTCCGATATCCAACCTTTGATTAGATCAGTTCTTGATGGATTCAATGTTTGCATTTTTGCATATGGACAAACTGGTTCAGGAAAAACATA
                                          tgataac  putative branch site (score: 11)
                                   ttttatttgataact  TA-rich tract