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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctttgactgcaaatcatgtctatcgacctggttctgattttagataaaatttcag

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G053644_T01 (Zea mays), 5'ss of exon 8
CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctttga-----ctgcaaatcatgtctatcgacctg--gttctgattttagataaaa----tttcag
|||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| |||||||||||||||||||||||||| ||  |||        |||||| |||||  | | || |||    ||||||| ||     ||    ||||||
CCCTCGCTGGTTGCTGAAGCAAGAGGT-CCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAGgtcagtccttcagttttcctgcaattcatggttctggaactgtaagtctgattatattcctaacatttttcag

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G386614_T01 (Zea mays), 5'ss of exon 1
CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctttga-----ctgcaaatcatgtctatcgacctg--gttctgattttagataaaa----tttcag
|||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| || ||||||||||||||||||||||| ||  |||        |||||| |||||  | | || |||    ||||||| ||     |     ||||||
CCCTCGCTGGTTGCTGAAGCAAGAGGTCCCAAAAGTTGTCAACTCTATCAACAGGCAGTTACGCGAAAAATCAATCAAGACAAAGgtcagtccttcagttttcctgcaattcatggttctggaactgtaagtctgattatattcctagcatttttcag

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G168629_T04 (Zea mays), 5'ss of exon 12
CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctttga-----ctgcaaatcatgtctatcgacctg--gttctgattttaga--taaaattt--cag
|||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| |||||||||||||||||||||||||| ||  |||        |||||| |||||  | | ||  ||    ||||||| ||    ||| ||||  |||
CCCTCGCTGGTTGCTGAAGCAAGAGGTCCCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAGgtcagtccttcagttttcctgcaattcatggttctggaattgtaagtctgattatattcctaacattttccag

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA07G40230.2 (Glycine max), 5'ss of exon 13
CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctttgactgcaaatcatgtctatcgacctggttctgattttagataaaatttcag-----------------
 ||| |||||||| |||| ||||||||  | ||| |||||||||| || ||||||||||||||||| ||||| ||||||||||||||       | | |  ||||   ||    | ||  | | |   ||| |    | ||||| ||                 
TCCTCGATGGTTGTTGAAGCAAGAAGTGTCGAAGATTGTCAAATCTATAAATAGGCAGTTGCGTGAGAAATCTATCAAGACAAAGgtag-----tagtcatcaaaagttgatagttgattttgattaaattatctccagaatttaagcatctttgtctatgcag

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA17G00570.1 (Glycine max), 5'ss of exon 12
CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtga-gctctttgactgcaaatcatgtctatcgacctggttct-----gattttagataaaatttcag------
 ||| |||||||| |||| ||||||||  | ||| |||||||||| || ||||||||||||||||| ||||| || |||||||||||     || |  |  |   || ||   | |||||    || |     |||||||   |  |||          
TCCTCGATGGTTGTTGAAGCAAGAAGTGTCAAAGATTGTCAAATCTATAAATAGGCAGTTGCGTGAGAAATCTATTAAGACAAAGgtagtagtcatcaaaagttgataattgatttcgactaaattatctccagattttaagcatcattgtctttgcag

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|88353222|gb|CI654488.1|CI654488
EST:     TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG                         GTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTG
genomic: TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctt ... aaaatttcagGTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTG
EST: gi|58669402|gb|CK058088.1|CK058088
EST:     TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG                         GTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGT
genomic: TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctt ... aaaatttcagGTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGT
EST: gi|88307071|gb|CI640503.1|CI640503
EST:     TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG                         GTTGGAGCATTCTCTGTATTGAAGGA
genomic: TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctt ... aaaatttcagGTTGGAGCATTCTCTGTATTGAAGGA
EST: gi|325494226|gb|JG458750.1|JG458750
EST:     TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG                         GTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGT
genomic: TTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctt ... aaaatttcagGTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGT

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), 75 (downstream exon)
Score: 29

CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAGgtgagctctt ... aaaatttcagGTTGGAGCATTCTCTGTATTGAAGGAGCTTGTTGTTGTACTGCCAGACTGTCTTGCTGATCATATTGGGTCACTTGTTCCTGGGATTGAGAAGGCTTTGA




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