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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA

Basic information

species Oryza sativa
transcript LOC_Os01g73790.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 2
gtgagtgcagtaactttt--------gttattcatg---tcattacctgaacactt----tgtaaccgtgtgctttt----tgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
|| |||  |||||  |||        |    | |||   |  ||     |||||||    | |     |||  ||||    ||||  |   |||||||| || ||||||||||||||||| |||||||| ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| ||||||||||||||
gtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATTGGATTGGGCCAAGGATGGATTTCATTCCTGGTGTCGATGGTCCTAGTGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
-------------------------gtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
                         |  | ||  ||| ||  || | ||| |    |    | ||    || |   | | |  || |||| | |  |||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||||||
gttagtaaattagcttgttatttttgccactgt-gtagctgatggtcttcct--tctcgttttaat-tattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA17G05440.1 (Glycine max), 3'ss of exon 2
-----gtgagtgcagtaacttttgttattcatgtcattacctgaa--cactttgtaaccgtgtgctttttgag------ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
      ||  |    |   |||  || || ||  |||   |||    ||  |  | ||| |   ||   ||||       | |   ||||||| || || ||||||||| | || |||||||||||||||||||| ||||||||||||||| ||||||| || ||||| ||  |||||||||| |||||
gtgagctgcttttgtttggtttaattttttattgcatatactgtttccatgtcttgacctttgtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGACCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGTCCAAGTGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
gtgagtgca---gtaacttttgtt---attcatgtcattacctgaacactttg-taaccgtg--tgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
||||||  |   |||  |||||||    |  ||||  ||  ||    | |||| |||   |   |  | | ||| | |   | |||||| || || ||||||||| | |||||||||||||| || || || || |||||||||||  ||||||| || ||||||||  |||||||||| |||||
gtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggc-agCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G30490.2 (Glycine max), 3'ss of exon 4
--------------gtgagtgcagtaacttttgttattca-tgtcattacctgaacactttgtaaccgtgtgctttttgag------ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
               |  ||  | |   || |    | || |||    |  |   ||  |  | ||| |   ||   ||||       | |   ||||||| || || ||||||||| | || |||||||||||||| ||||| ||||||||||||||| ||||||| || ||||| ||  ||||||| || |||||
gtgagctgattttgtttggtttaattttttattgcgtacactgtttccattttttcatgtcttgacctttgtctcactgagatgacattgttggcagCTGAGGGTGCTGAAAATGGCTTGGAATTCACAATTGTGAGGCCTTTTAATTGGATTGGACCACGAATGGATTTCATTCCCGGCATTGATGGCCCAAGTGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G08930.1 (Glycine max), 3'ss of exon 4
gtgagtgcagtaacttttgttattca--tgtcattacctgaacactttgt-aaccgtgtg----ctttttgagctttaac------cagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
||||||   | |  | || || || |  |||  ||   |     |||| | ||   |||     ||   |||  | | |       ||||||| || || ||||||||| | ||||||||||||||||| ||||| || |||||||||||  ||||||| || ||||||||  |||||||||| |||||
gtgagttttg-atttgtttttgtttaggtgttgtttttttttttctttttcaattttgttaattctcactgatgtgtgattattggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTGAGGCCTTTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGCATTGATGGTCCAAGTGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------gtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
              |    | |  || |||| |  |||  | ||  |    || | ||| | ||       ||||   | |     ||||||| || || || ||||| || |||||||| ||||| ||||| ||||| ||||||||||| || ||||| || || |||||  ||||||||||||| ||
gtatgtagttttcttacacgaaagaaattttttgtttctagacacaa----aaaagtttctcacgtcacttttttctggttg----cagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gtgagtgcagtaacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
                   ||          | ||   || | |||  |  | |  |  |||   |    | |  ||||| |   || || |||||| || || || |||| ||| |||||||| |||||||| || || || |||||||| || |||||||| |||||||||||  ||||||||||||| ||
gtgagtgaacttttccatcgatctgtacgtttcttagcatgcgtgt-gtatcatacatccttctcatttttattttttttcattgtttac-agCTGAGGGTGCTGAGAATGACCTAGAGTTCACCATTGTGAGGCCCTTTAACTGGATTGGGCCCAGAATGGATTTTATTCCTGGCATTGATGGTCCTAGCGA

upper sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
----------------gtgagtgcag-taacttttgttattcatgtcattacctgaacactttgtaaccgtgtgctttttgagctt-taaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
                 | | |   | |   | ||   || |||    |  | |  |  |||| |||   | |  || ||    || |   |||||||||| ||||| |||||||| |||||||| |||||||| ||||| || |||||||| || |||||||| || ||||||||  ||||||||||||||||
gtgagtcaacttttccatcaatctggatgtttcttaacatgcat-ctgtctcatagat-ctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA

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|58677005|gb|CK065692.1|CK065692
EST:     GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG                         CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST: gi|58675034|gb|CK063721.1|CK063721
EST:     GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG                         CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST: gi|58587635|gb|CF985943.1|CF985943
EST:     GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG                         CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST: gi|58587411|gb|CF985719.1|CF985719
EST:     GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG                         CTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATT
EST: gi|58655446|gb|CK044126.1|CK044126
EST:     GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTG                         CTGAAGGAGCAGAAGAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAAT
genomic: GCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAA-AATGGCCTTGAGTTCACAATTGTGAGACCTTTCAAT

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: 73 (upstream exon), 64 (downstream exon)
Score: 13

GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgcag ... ctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatgtcattacctgaacactttgtaaccgtgtgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA
                       ttgtaac  putative branch site (score: 13)
                      tttgtaa  TA-rich tract