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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttttacattcaatttgtcttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g50440.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G090172_T02 (Zea mays), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataa-cacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttttacattcaatttgtcttgcag
||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| |||||||| || | ||  ||||||    |||||   | | ||||| |||   |||  ||||||   | ||  ||||||  |   ||| | ||||||
TGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATATATGCGGTCCTGGACAGGAACTATCATTGGTCCTCCCAATgtatgctgcagaaatacccatagtgagatacataatacattttctttattattttcaaacctga-gaggttttac--tgcgtttattttgcag

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataa-cacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttttacattcaatttgtcttgcag
||||||||||||||||||||| || ||||||||||| ||||| |||||||||||||||| |||||| ||||||||||||||||||||||| ||||| || ||||| |  | ||  |||||| | ||||||   | |||||||| ||   ||| |||||||   | ||| ||| || | || |||   | ||||
TGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATTTATGCGGTCCTGGACAGGAACTATCATTGGTCCTCCCAACgtatgctacagaaatacccataactagatacataatgcatttgttttgttattctcaaacctga-gatgtttcac-tgcatttt---tcgcag

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA07G24950.4 (Glycine max), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgta---tgttgtataacacccatta---gtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttttacattcaatttgtcttgcag---
||||||||| ||||| ||||| || || |||||||||||||||||||||||||||||||| ||||  || ||||| || |||||||| || || |||| ||||   || ||| |   |    | |    | |  ||   | ||        || | ||||   | |||   |     ||  || |||||   | |  |   
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGACATATACATGCAATCTTGGACTGGGACTATCATCGGTCCCCCTAGTgtaagttgctgtctgttatttttgacacattggaatccccagctaacatccctatttgcttcta-tgacaaagtaaatattttgaatttcagtgggggctt

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G04710.1 (Glycine max), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttttacattca-atttgtcttgcag---------
||||||||| ||||| ||||| || || ||||| |||||||||||||||||||| || || ||||  |||||||| || ||||| |||||||| |||  |||| | | |        | || |   |  |    | || |     |    |    ||| || |  |  | |||  || | |    | |   ||         
TGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTACATGCAGTCCTGGACTGGGACTATTATTGGCCCCCCTGGTgtaagcttttc--tgttctttggagaaattctgttacaatgataacatctttgcaaaattgcagaacttattatttttatagaaatttaagagtctacggct

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G35000.1 (Glycine max), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatat-taactgcatttgcttctgt-----atgctcaaactgaatgatcttttacat-tcaatttgtcttgcag-
||||||||| ||||| ||||| || || |||||||||||||||||||||||||| || || ||||  |||||||| || ||||| |||||||| |||  |||| | |||      |     |  |  | | | |||       | ||| |     ||  |  |||| | |  | || || |  |  ||  || ||     
TGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTACATGCAGTCCTGGACTGGGACTATTATTGGCCCCCCTGGTgtaagctgtcctgttctttggaaaaattgtgttactatgaaaacctctttgcaaaattgtagaacttactatttttatagaaatttatgagttttatcaa

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatct---tttacattcaatttgtcttgcag------
||||||||| ||||| ||||| || || ||||||||||||||||| ||||| |||||||| ||||  || ||||| || ||||||||||| || |||  |||| | ||       |   |  | | ||| ||| |   ||| ||| | |  | |     |||   ||     | | ||   ||  |  ||  |||      
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctg-aaataataatttatttttcttttattagttatttttgacacattggaatctccagctaacatccctatcagcttcta

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaact-gcatttgcttctgtatgctcaaactgaatgatcttttacattcaatttgtcttgcag-------
|||||| || ||||| ||||| || || |||||||||||||||||||||||||| || |||||||  || ||||| || || ||  |||| |||||||||||||||        | | ||   |   | ||   |   ||||   | ||| || |  |    |       |||  |     |||||     |        
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT1G70660.1 (Arabidopsis thaliana), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttttacattca-atttgtcttgcag-------
|||||| || ||||| |||||||||||||| ||||||||||||||||||||||| || |  ||||  || ||||| || || ||  |||| |||| ||||||  ||| | |    | || |        | | ||    ||     |  ||| | | |   |  |    |||  ||  | ||   | ||  |        
TGAGAAAGGAATTGGAGATGGGACAGTGAGTTATGGAATGGATGATGCTGATGATATTTTGATGCAATCTTGGACTGGTACCATTCTTGGTCCTCATAATgttagttttcttcttctcaatctatctcttcatcttttgtttaacttaaatgataatatctatggtagatttgaataaagatgcattttttaatgctaaa

upper sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 5'ss of exon 2
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtata--------acacccattagtagatattaactgcatttgcttctgtatgctcaaactgaatgatcttt-tacattcaatttgtcttgcag
 || ||||| ||||| ||||| || || || ||||||||||||||||||||||| ||||| ||||  || ||||| || ||||||||||| |||||||||||  ||| | |         |||    | |  | ||| | |   | ||      || ||     ||||  ||| |     |  ||    || || ||    
GGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttttctttttcacacaattttcatgatataatgaactccttacaggttgaatctctcaactagatgttaagaatttatgtggttggtattatc-

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|27545659|gb|CA763865.2|CA763865
EST:     ATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAAT                         ACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
genomic: ATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgta ... tgtcttgcagACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
EST: gi|88242402|gb|CI242251.1|CI242251
EST:     AGGAACTATCATTGGCCCTCCTAAT                         ACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
genomic: AGGAACTATCATTGGCCCTCCTAATgtatgttgta ... tgtcttgcagACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
EST: gi|88415272|gb|CI586478.1|CI586478
EST:     ATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAAT                         ACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
genomic: ATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgta ... tgtcttgcagACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
EST: gi|58592031|gb|CF990339.1|CF990339
EST:     ATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAAT                         ACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
genomic: ATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgta ... tgtcttgcagACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
EST: gi|58691622|gb|CK080309.1|CK080309
EST:     GTTCCTGGACAGGAACTATCATTGGCCCTCCTAAT                         ACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC
genomic: GTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgta ... tgtcttgcagACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGAC

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: 61 (upstream exon), 61 (downstream exon)
Score: 25

TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgta ... tgtcttgcagACTGTTCATGAGGGACGAATCTATCAGTTGAAGTTGTTCTGTGATACAGACTATCCAGACAGACCACCTACTGTTCGATTCCAGACTCGAATCAATATGT




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