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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatctgcagtgaattatcttgtgagtatattggacattgttacgagacacttcgttgaatcag

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G124886_T04 (Zea mays), 5'ss of exon 7
CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatctgcagtgaattat---cttgtgagtatat-tggacattgtt-----acgagacacttcgttgaatcag
|||| ||||||||||||| |||||||| || |||||||||||||| |||||||||||||| |||||| ||||||| ||||||||||||||||| || ||||| || |||  ||| |||||| |   | |||||  || | || ||  |||      | || |   ||  |  ||||||
CACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACCTAATTACTGGCTCTGATGATCAGACTGCAAAGgtttgtcataagcactgaattgtactcctgtgatcatgtctgtactctgtacactgatgacattattgatcaaatcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G141587_T01 (Zea mays), 5'ss of exon 7
CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatctg---cagtgaattat---cttgtgagtatat-tggacattgttacgagacacttcgttgaatcag
|||| ||||||||||||| |||||||| || |||||||||||||| ||||||||||| || |||||||||||||| ||||||||||||||||| || ||||| || ||| ||   || |||||| |   | ||||   ||   || ||  ||| | || |   || ||  ||||||
CACACTAGATGGCCATTCGAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGACCGACCATACTTAATTACTGGCTCTGATGATCAGACTGCAAAGgtttgtcatatgatgcactgaattgtactcctgtggtcatgcatgcactctgtgatgacattattggtcaaatcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 7
CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatg----ccatctgcagtgaattatcttgtgagtata--ttggacattgttacg-agacacttcgttgaatcag-------------------------------
 || || |||| ||||  |||||| || |||||||||||||||||||| ||||||||    || ||| | || || || ||||||||||| || || ||||| ||    | || | | ||   ||  ||  | |   |   ||  |  | ||| |  | |    |   || ||  |                               
TACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACCTGATAACTGGTTCTGATGATCACACTGCCAAGgtttgttttctattttctgtttttttcctcttcatcttccctttaatttggttgcctatatgtgtatatggataggaattattatgccaataaaacctttgaaacag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 7
CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatctgcagtgaattatcttgtgagtatattggacattgttacgagacacttcgttgaatcag-------------------------------------
 ||||| ||||  |||  |||||| || |||||||||||||||||||| ||||||||    || ||  |||| || || ||||||||||| || || ||||| ||   |||    |   || | |  |    || ||     |  ||  |   |   |  ||| ||  |                                     
TACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATCTAATAACTGGTTCTGATGATCACACTGCCAAGgtttgttttctattttctgttttttcctcttcatcttccctctaatttggtttcctatatttgtatatggataggaattattatgccgataaaacctttgaatcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 5'ss of exon 7
CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatctgcagtgaattatcttgtgagtatattggacattgttacgagacacttcgttgaatcag------------------------------
 ||||| |||| ||||   ||||| || |||||||| ||||| || || |||||||||   || || |||||||| |||||||||||||| || || ||||||||||  |||   | |||  |||| | |||  ||   |||||  |||  |||| |  ||    ||||                              
TACATTGGATGCCCATCAGAAAGGAGTAAATTGTGTAGATTATTTCACCGGTGGTGATAAGCCCTATTTAATTACCGGCTCTGATGATCACACTGCTAAGgtatgcctcctgt--tcaatggtctttt-agttgat---acatttctactggacattatgtgctttcaggttatttactagttgaatttcgtgaatcag

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 7
CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatctgcagtgaattatcttgtgagtatat-----tggacattgttacgagacacttcgttgaatcag---------------
 || || |||| |||    ||||| || || |||||||||||||| |||||||||||    ||||||||||| || || ||||||||||| || || ||||| |   |||||  |   |||  ||    ||  |       ||  ||||          ||||  |   || |                
TACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACTTAATCACGGGTTCTGATGATCAAACTGCCAAGgtgt-ttatctgatgcttattgactaaatagcttccatttatgtgcattccatttgattactttctgtgattaaattttggtggaacag

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|300215876|gb|HO088502.1|HO088502
EST:     GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAG                         GTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
genomic: GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
EST: gi|29680637|gb|CB676912.1|CB676912
EST:     GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAG                         GTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
genomic: GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
EST: gi|29671007|gb|CB667282.1|CB667282
EST:     GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAG                         GTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
genomic: GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
EST: gi|88726867|gb|CI750522.1|CI750522
EST:     GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAG                         GTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
genomic: GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
EST: gi|29613910|gb|CB618923.1|CB618923
EST:     GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAG                         GTTTGGGACTATCAAACAAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
genomic: GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCA
EST: gi|29680636|gb|CB676911.1|CB676911
EST:     GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAG                         GTTTGGGACTATC
genomic: GTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATC

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), 72 (downstream exon)
Score: 32

CACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACTTAATTACAGGCTCTGATGATCAGACCGCGAAGgtatgccatc ... gttgaatcagGTTTGGGACTATCAAACGAAGAGCTGTGTTCAAACGCTTGAAGGACATGCACATAATGTCTCTGCTGTTTGTTTCCATCCGGAGTTACCTATAATACTTA




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