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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC

Basic information

species Oryza sativa
transcript LOC_Os01g15460.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086994_T03 (Zea mays), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |||| ||      ||||| ||  || || | ||||  |||||||    || | |  ||   |  ||| |||||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| |||||       
gtatgagaattctcctatggatgtgcttctttgta-acat-ttttaactgtttttgggaaaaaa--tttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCG-------

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086994_T01 (Zea mays), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |||| ||      ||||| ||  || || | ||||  |||||||    || | |  ||   |  ||| |||||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| ||||| | ||||
gtatgagaattctcctatggatgtgcttctttgta-acat-ttttaactgtttttgggaaaaaa--tttacattaatgaaatgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTAACCC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G036837_T02 (Zea mays), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |||| ||  ||  || || ||        | ||||   | || |   ||| |    |||  |  ||| || ||||||||||||| || ||||||||||| ||||| ||||||||||| || |||||  ||||||||||||| |||||||| ||||| |||||| ||||| ||||||
gtatgagaattctcctatgattgtgtttcttgga-----ttttttaagtattattggaaaaaataattgacattaatgaagtgcagGGTGAGAAAGAATGCTCCTACTATATGAAGACTGGGCAATGCAAGTTTGGTTCTACATGTAAATTTCATCATCCAGAATTTGGTGGTATTCCGGTGACCC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G17250.1 (Glycine max), 3'ss of exon 4
gtgtgaaatctc-tcgtaaaatattgcttattcatac-acttgtttttcctgttttgaaaaag-agatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| |||    || |  |    |  |||| || |||   || |        |  |   |      | |   ||       |  ||  ||||||||||| ||||||||||||||  ||||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtatgactcttcgttttgctcttctgctcatccatgttacctacagaaaataatgcaattggttaaaccatgccttttgtttaa-acagGGTGAGAAAGAGTGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G02550.1 (Glycine max), 3'ss of exon 4
gtgtgaaatctctcgtaaaatat-tgcttattcatac-acttgtttttcctgttt-tgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| |||    |||  |      | ||||  |||||   || |        |   | | |  |  | |   ||       |  ||  ||||||||||| || |||||||||||  | ||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtttgactcttctttttgctcttctgctcgttcatgttacctacaccaaataaatgtaatgattaaaccatgccttttgtttaa-acagGGTGAGAAAGAATGCTCCTACTATTTAAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCTGCTGGCACATCATTGCCAA

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G28820.1 (Glycine max), 3'ss of exon 4
-------------------------------------gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                     |  ||   |     ||    | ||| ||  | || ||      | |  || |  ||    || |||||  || | || | |  ||||||||||||||||| ||||| ||  ||||||| || ||||| || |||||  | || ||||||||||||||||| |     | |||  | |  ||  | |
gtctgtatcactttttgtatttactacataaggctaggcatgcttttgaatgttctgttttgttttctgat-catggaaatattttgatccgagtttga-atgtttataaatatgata-acagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCATCCAAATTCCAC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G37980.1 (Glycine max), 3'ss of exon 4
----------gtgtgaaatctct-cgtaaaatattgctta-ttcatacactt----gtttttcctgttttgaaaa----agagatgttggtacaaataaaat--------------gcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
          || ||   |  || ||||||||  ||  |  ||  |  | ||    ||   || | |  | |  |     ||  | ||| |  || |  |||               |||||| |||| ||||| ||||| ||| |||||||||| || || || |||||  | || |||||||||||||||||  |    |  || || |   |     
gtctgtatcagtttgtgtttactgcgtaaaattatgtgtgctttgtgaattttggtgtcactcttttcctaacgatgatggaagttttgttcaaacttgaattttcgtgcatgataacagGGTCAGAAAGAGTGTTCCTATTACGTGAAAACTGGACAGTGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCACAGCCTGCAGGCGTCCAAGTTCTAG

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G10230.1 (Glycine max), 3'ss of exon 4
----------------------------------gtgtgaaatctctcgtaaaatattgcttat----tcatacacttgtttt-tcctgttttgaaaaagagatgttggtaca-aataa--aatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                  |     | | | | || ||   |   || |    ||  ||| | |     |  || | ||||   || |||||  || |  ||||  |   ||||||||||||||||| ||||| ||  ||||||| || ||||| || |||||  | || ||||||||||||||||| |     | ||| || |  ||  |  
gtctgtgtcacttttttgaatttacttacataaggctaagagtgttttgtgaatgttcagttttgttttctgacagtggaaagattttgatctgaatttga-atgtttataaatgataatgataacagGGTGAGAAGGAGTGTTCCTATTATGTGAAAACAGGACAATGCAAGTTTGGTGCAACTTGTAAATTCCATCATCCAGTTCCTGCTGGCGTCCAAATTCCAG

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G17260.2 (Glycine max), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaa-gagatgttggtacaaataaaatg------cagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
|| ||| |  |  |      | |||||  |       || || |           ||  | |  |||||   |||       ||      ||||||||||| || |||||||||||  ||||||| ||||| || |||||||| |   | |||||||||||||||||  ||   | |||     |  || |  
gtatgataa-tgacacttcttgttgctcttcttctgcctcgtgtaattgacagcaaatgatgcaatgttaaaacatgccttttgtttaaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAATTTGGTATATCTTGTAAATTCCATCATCCTCAACCGGCTGGCACATCATTGCCAG

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G47850.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
  || |  | | |    |   || |   | | | |  || || |   |   |||| |     ||| ||  || |||     || ||||||| || || |||||||||||  ||||||| |||||||| |||||||| |  || |||||||| ||||||||  |    | ||||  | |  |  | |
--gtaagctttgtttccactcat-gtcaaataaaaggctagtct---cgagtttgcat----gatcttt-tataaactctttgtagGGTGATAACGAATGCTCCTACTATTTGAAAACGGGGCAATGCAAATTTGGTATAACCTGTAAATTTCATCATCCTCAGCCTGCTGGTACTACTGTCCCAC

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G47850.2 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgaaatctctcgtaaaatattgcttattcatacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC------------------------------------------------------------------------------
  || |  | | |    |   || |   | | | |  || || |   |   |||| |     ||| ||  || |||     || ||||||| || || |||||||||||  ||||||| |||||||| |||||||| |  || |||||||| ||||||||  |    | ||||  | |  |  | |                                                                              
--gtaagctttgtttccactcat-gtcaaataaaaggctagtct---cgagtttgcat----gatcttt-tataaactctttgtagggtgataacgaatgctcctactatttgaaaacggggcaatgcaaatttggtataacctgtaaatttcatcatcctcagCCTGCTGGTACTACTGTCCCACCACCACCAGCATCTGCACCTCAGTTTTATCCATCGGTGCAGTCACTTATGCCTGACCAGTATGGAGGTCCATCTTCTA

upper sequence: LOC_Os01g15460.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0104g01460.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------gtgtgaaatctctcgtaaaatatt-gcttattcatacacttgtttttcctgttttgaaaaagag-atgttggtacaaataaaat------gcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                 | ||||   |  ||  | ||  || |  |  ||   | |   |      ||  |   ||   |||||  |  |    ||||       ||||||||||| || |||||||||||  ||||||| ||||| || || ||||| |  ||||||||||||||||||||  ||   | |||     |  || |  
gttgggatttggtttattcttcaccttttctaatcaaattcgttttactaaatcagcatggttgtaatttgggaatggacacttccatttagcttatgtttatgaattggaaattttgcaacagGGTGAGAAAGAATGCTCCTACTATTTGAAAACGGGGCAGTGCAAGTTTGGTATAACATGTAAATTCCATCATCCTCAACCAGCTGGCACATCATTGCCAG

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|88572959|gb|CI664530.1|CI664530
EST:     GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTG                         GGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
genomic: GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
EST: gi|88306285|gb|CI636670.1|CI636670
EST:     GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTG                         GGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
genomic: GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
EST: gi|88306241|gb|CI636626.1|CI636626
EST:     GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTG                         GGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA
genomic: GAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGA

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), 73 (downstream exon)
Score: 20

GACTTGCAAATTTGGTACCAATTGCAAATATCACCATCCTAAGCAAGATGGAGCTGTGCTACCTGTTATGTTAAACAACAGTGGATTCCCTATACGCCTGgtgtgaaatc ... taaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacacttgtttttcctgttttgaaaaagagatgttggtacaaataaaatgcagGGTGAGAAGGAGTGCTCCTACTACATGAAAACTGGGCAATGTAAATTTGGAACTACATGTAAATTCCATCATCCGGAATTCGGTGGTGTTCCGATGACCC
                                       tacaaataaaat  TA-rich tract