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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttattgcagttattcacctaacagctcatatgcaattgtggagtgatgtttgttttcctggggatgctcccccctccccccccccttccctttttcctccctctctctctgagtacacagtagtgtttggctgctccgcttaccattttgtcttttttggtag

Basic information

species Oryza sativa
transcript LOC_Os01g36930.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G028733_T02 (Zea mays), 5'ss of exon 10
GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttattgcagttattcacctaacagctcatatgcaattgtggagtgatgtttgttttcctggggatgctcccccctccccccccccttccctttttcctccctctctctctgagtacacagtagtgtttggctgctccgcttaccattttgtcttttttggtag
|||||||||||||||||||| || ||||||||||||||||||||||||||||| |||||  ||||||||  ||||   ||  || ||  |         |  |        | | || ||  |  |  |     ||    ||| |         || |    |   ||                                                                 
GATGCAGAAGAATGCTGGACACAGTTGGTGTATACACTTTCTCAAACTCTTACCTCAGATTCAAGgtaacatatt--cgtcgttaactgatggaacttcaccctgccacc-acttatattcatcatatttatcttgtggtcccttttttagattctacaaagtggact-----------------------------------------------------------------

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G017086_T01 (Zea mays), 5'ss of exon 8
GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttattgcagttattcacctaacagctcatatgcaattgtggagtgatgtttgttttcctggggatgctcccccctccccccccccttccctttttcctccctctctctctgagtacacagtagtgtttggctgctccgcttaccatt--ttgtcttttttggtag-------
|||||||||||||||||||| || ||||||||||| ||||||||||||||||| |||||  ||||||||  | ||                    |  | |  || |||  | | |||  | ||  ||| |  |    |     |      |   ||  |||| || ||||| |   | |      |  | | ||||||||| ||  || ||  |||  ||| ||  |||  |         
GATGCAGAAGAATGCTGGACACAGTTGGTGTATACGCTTTCTCAAACTCTTACCTCAGATTCAAGgtaacctgtt--------------------tgttgtcaaaatgtcaactaatggctcttcaccttgtaa---ccatttatatttatcgtattatctttgtcttccctgtaatttt-----tatggcaatgtttggctactttgcctaaaattatttgcctactttttttttctatag

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G028733_T01 (Zea mays), 5'ss of exon 8
GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttattgcagttattcacctaacagctcatatgcaattgtggagtgatgtttgttttcctggggatgctcccccctccccccccccttccctttttcctccctctctctctgagtacacagtagtgtttggctgctccgcttaccatt--ttgtcttttttggtag---------
|||||||||||||||||||| || ||||||||||||||||||||||||||||| |||||  ||||||||  ||||   ||  || ||  |         |  |        | | || ||  |  |  |     ||    ||| |         || |    |   |||||| |   | |      |  | | ||||||||| || ||| ||  | |  ||| ||  |||  |           
GATGCAGAAGAATGCTGGACACAGTTGGTGTATACACTTTCTCAAACTCTTACCTCAGATTCAAGgtaacatatt--cgtcgttaactgatggaacttcaccctgccacc-acttatattcatcatatttatcttgtggtcccttttttagattctacaaagtggactccctgtaatttt-----tatggcaatgtttggctacttcgcctaaaactatttgcctccttttttttttcctatag

upper sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 8
lower sequence: EFJ12930 (Selaginella moellendorffii), 5'ss of exon 7
--------------------------GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttattgcagttattcacctaacagctcatatgcaattgtggagtgatgtttgttttcctggggatgctcccccctccccccccccttccctttttcctccctctctctctgagtacacagtagtgtttggctgctccgcttaccattttgtcttttttggtag
                          ||||| |||||||||||||| ||| | |||||||||||||||||   | |     ||    |  |  |    |   | |   || || |      |||    |   |||||  |  | ||  |||  ||                                                                                                        
CCAACAATGGAGCTTACATGCAGCAGGATGCGGAAGAATGCTGGACGCAACTCGTGTATACACTTTCTCAGCGTTTGCGGCCATCTTCTGGAGAGACCAGgtccgc-gtttacttg-----tcactgactgatgtggtatt-tcttaatttctctaccag---------------------------------------------------------------------------------------------------

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|163920010|gb|EG709816.1|EG709816
EST:     TGGA-CCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
EST: gi|29646291|gb|CB651298.1|CB651298
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGA
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGA
EST: gi|29679500|gb|CB675775.1|CB675775
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
EST: gi|29615418|gb|CB620430.1|CB620430
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
EST: gi|29674105|gb|CB670380.1|CB670380
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
EST: gi|58601182|gb|CK011710.1|CK011710
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
EST: gi|218489926|gb|FG960730.1|FG960730
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
EST: gi|3766733|gb|AU030843.1|AU030843
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAACCAAG                         TGAACCTCCTGCTGGTCNAATGAAGGA-CTTTTTGGGGTTGATCCCGTGA
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGA
EST: gi|29615343|gb|CB620355.1|CB620355
EST:     TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAG                         TGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG
genomic: TGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAG

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: 48 (upstream exon), 73 (downstream exon)
Score: 37

GATGCAGAAGAATGCTGGACCCAATTGGTGTATACACTTTCTCAAACTCTTACATCAGAAACAAGgtaatttatt ... tttttggtagTGAACCTCCTGCTGGTCAAATGAAGGAACTTTTTGGGATTGATCTCGTGAGCAG




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