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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttgacctaggatcagattcacaagcaataagggattgtctccttgctattctca...

Basic information

species Oryza sativa
transcript LOC_Os01g64650.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G446711_T01 (Zea mays), 5'ss of exon 2
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttgacctaggatcag-attcacaagcaataagggattgtctccttgctattctca
|||||||||||||||| ||||| || ||||| ||||| ||||||||||| ||||||||||| ||||||||||  ||||||||||||||||||||| |||||  |  | || | |   | | |||    |  | |  | ||   ||| | ||  | | |  | |   ||||  ||     |   ||  |     |  |||
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCAGTTGCATTCATGGATGATCATTATCCTGTACAGAGTGCATTTTCTCTTCTGAATCAGgtaccattcgttatccactagactcccacttgcctttgcttttggtttaagctcaggttaccaattgtaagctgtagccagtca-cttttcatcctgttca

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G178244_T01 (Zea mays), 5'ss of exon 2
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttgacctaggatcag-attcacaagcaataagggattgtctccttgctattctca
|||| ||||| ||||| |||||||| ||||| ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||||||| |||||    || |  ||| ||| |||||   ||  | |  | ||   ||  |  |  | | |  | |   |||   ||     |  | ||    | | |    
AATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAGgtaccgaccatgattcctgagattcccacatgtctttgcttttggttgaagttgagtttaccaattgtaagttgtagccagtcatttctcacccagttct-

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G387076_T02 (Zea mays), 5'ss of exon 3
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttga--cctaggatcagattcacaagcaataagggattg-tctccttgctattctca
|||||||||||||||| ||||| || ||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||| |||||  |  | || | |   | | |||    |  | | | ||| |  || |  || ||| |   | |   ||||  ||     |   | | | | || |||   
AATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAGgtaccaatcgttatcccctagactcccacttgccttttgcttttggtttaagcccaggttaccaattgtaagctgtagccagtcacttttcattctgttc---

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G19950.1 (Glycine max), 5'ss of exon 2
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttgacctaggatcagattcacaagcaataagggattgtctccttgctattctca---
| |||||||| ||| || ||||||| ||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||  ||||  || |     |   ||       | |  |||   ||| | |    ||| |   ||  | | |    | ||    |||   | |  ||   |    ||   
AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAGgtgaga-ctcagatcactgttggatttttgctgct--tccgtattcaagacatgttattcgttgctttggaaaattaggaagatattgtttgaaggtgcatga

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G13840.1 (Glycine max), 5'ss of exon 2
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcc------tttgttcttga--cattcctgtattgcatatccttgtatttgacctaggatcagattcacaag--caataagggattgtctccttgctattctca
| |||||||| ||| || ||||||||||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||| ||||  ||  |          || |||   || | || ||||| ||||   | |   ||   |    |    | |       | |||||| | | | | | |          
AGTACAAGGTGCACACATACAACAGGAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAATCAGgtgagactcagataaccgtttattggttcagtgctatattgtatatttgtattcatggaattttgttgcttcctttgtgtctataaggaacttttttcat----------

upper sequence: LOC_Os01g64650.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 5'ss of exon 2
AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcctttgttcttgacattcctgtattgcatatccttgtatttgacctaggatcagattcacaagcaataagggattgtctccttgctattctca---
|||| || || || ||  ||||||| ||||||||||| ||| | |  ||||||||||| ||||||||||| ||||| ||||||||  | || ||  |||||  | ||  | ||  || | || |||| ||   | |  |   |    |  |  |||   ||| |   |  |||    |||   |   |  ||     |   
AATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAGgta-aacccaatttttatggctttactgtctttgtttttttcaaaagaaatttcagat--aattgatctggcatactttatttcttttgttttaagtcaacca

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|86601691|gb|CI256196.1|CI256196
EST:     TTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
EST: gi|218482998|gb|FG956126.1|FG956126
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
EST: gi|4879970|gb|AU064269.1|AU064269
EST:     TATGGATGATCACTATCCTGTACGA-GTGCAATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGTTTTCGGGGACT
genomic: TATGGATGATCACTATCCTGTACGAAGTGCA-TTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACT
EST: gi|38468730|gb|CF952861.1|CF952861
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
EST: gi|88243877|gb|CI242999.1|CI242999
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
EST: gi|218479888|gb|FG958307.1|FG958307
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
EST: gi|27578119|gb|CB000814.1|CB000814
EST:     TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG                         GTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA
genomic: TTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACA

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: 75 (upstream exon), 68 (downstream exon)
Score: 64

AATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAGgtatgagcct ... ttttatgaagGTACTTGACGAATACCAGAAGGCTTTCGGGGACTCTTGGAAAGCTGCTACAAAAGATGCAACAGATGCTGCCCAACAGTGGCCTTTCTTGACAGATGCTT




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