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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA

Basic information

species Oryza sativa
transcript LOC_Os03g01850.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 4
------------------------------gtactatagatt--tgtgttcaacattttgttttcttcataaag--tacatttttttttcgtcataaagttcatttt--tcatttaccttttc----tatacactag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                              | | | |  |||    ||||    |      | |  | |   |    | | || |   |   || ||  || |      | |  || | |||     ||||  |||| |||||||| ||||| |  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| || || |||||| |  |||||||||| |||||||||||| ||||||| || || ||||||||||| ||||
gtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggattcccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATTCTGCTTGGAGCGCGGCAGTATTCCACACCAGTTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAA

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143213_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttt-tcgtcataaagttcatttttcatttaccttttctataca--ctag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGT-TGGTTGTATCTTTGCAGAAA
                                              | | |||    ||  |   || || ||||          ||    ||   |     ||   | |    ||| |  |||   | |||  | |  |  |||| || || ||||||  ||  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| |||||||||||| | || |||||||| |||||||||||  | ||||| || ||| ||||||||||| ||| 
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactca--atacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAA-

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttt-tcgtcataaagttcatttttcatttaccttttctataca--ctag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                              | | |||    ||  |   || || ||||          ||    ||   |     ||   | |    ||| |  |||   | |||  | |  |  |||| || || ||||||  ||  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| |||||||||||| | || |||||||| |||||||||||  | ||||| ||                    
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactca--atacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTG-------------------

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 3
gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                  | | ||| || |  | ||||      ||||| |    |   |  |      |  | |||  |    ||    |    |   ||   | |||  | | ||| | |||| |||||  ||||||| |||||||| || ||  | ||||||||  | ||||||||||| ||||||||||| |||||||| || || || |||||||| |
---------------------------------cttaaaaaatataaatctttt-----gtaaaggtataatggtagatggacagtaaaaacatcaaattatctttttctgagttataaatttggcgattgtttgt-agGTGGTAACACTGTGGTACAGAGCTCCGGAAATTTTGCTTGGATCCCGTCAGTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                 ||  |  |  |  | || |  | | |     | | |||||| |  ||  |||  |||  | |  | ||||   ||    |  ||    || ||   |  |||  |||| || || || ||||| ||||||||||| ||  | ||||||||  | || |||||||| ||||||||| | |||||||| || ||||| |||||||| |
--------------------------------ttttgtggaa-aggtattgtggtaggctggttgatgatttttaacgtaa-tttaatatttatt--cccatt---tctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA

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|29662032|gb|CB658307.1|CB658307
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCATGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCATGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG




















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: 53 (upstream exon), 72 (downstream exon)
Score: 8

TCAGAATTTATTGATAGATCGGCGTACTAATACACTGAAGCTTGCAGACTTTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCATGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                   aactcac  putative branch site (score: 8)
                                             tatttttc  putative PPT
                                          aagtattttt  TA-rich tract