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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggactttggttcctgatatcagctacaattgccaatattttgctcatgatgtactcatgctagtttgattgctatgtctcatgttcgtactgtgctgtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG

Basic information

species Oryza sativa
transcript LOC_Os04g53190.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 8
gtaggactttggttcctgatatcagctacaattgccaatattttgctcatgatgtactcatgc-tagtttgattgctatgtctcatgttcg-tactgtgctgtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG
                     |  | |    |    | ||| | ||      | ||||    | | ||   |||  | || || |||   | || |||     || |||||||||| |||||||| ||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||||||| |||||||||||||   ||| | 
--------------------gtatgtttttttccttactatctggcc---agtatacttgcacattgtgaaattattgtgccttatgcatgataatgttgatgggatgcagGAGGTGCTGCTTCCAGGTGGCCATGGCCTCATGGTTCGTGGATATCGTCCAGTTATAAATACTCTTGCAAAAGGCTTAGATATACGCCTCAACCATAA

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G000052_T01 (Zea mays), 3'ss of exon 8
gtaggactttggttcctgatatcagctacaattgccaatattttgctcatgatgtactcatgctagtttgattgctatgtctcatgttcgtactgtgctgt--gggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG
                   |||  | |    |||         ||  ||  ||     |    || |  |||| || || || ||      |   || ||   || || ||||||| |||||||| ||||||||||| |||||||||||||| |||||||| || ||||||||||| ||||||||| |||||||||||||   ||| | 
------------------gtatgggtttt--ttggtttgtcgctggccagtatacgtgcgcatta-tgagattactgtgccttattacatgataatgttgacgggatgtagGAGGTGCTGCTTCCAGGTGGCCATGGCCTCATGGTTCGTGGGTATCGTCCGGTTATAAATACTCTCGCAAAAGGCTTAGATATACGCCTCAACCATAA

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G41570.2 (Glycine max), 3'ss of exon 7
gtaggactttggttcctgatatcagctacaattgccaatattttgctcatgatgtactcatgctagtttgattgctatgtctcatgttcgtactgtgctgtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG
         |        |  | ||||    ||     | | || ||  |||  ||||| | ||  | | | |  | | |   ||     | |||   |||   | |||||||||||||| |||||||| |||||||| ||||| ||||| ||    || ||  ||||||  || || || || || ||||| ||  | || |||||
---------taaccaacaa-gtaagct-tttttttttctttctttcttttgaattactcttccttctataaattat-tattatatcactcttctggtgtgtatttacaggagGTACTGCTCCCTGGTGGTCATGGTCTTATGGTCCGTGGCTACTTGCCTGTTGTAAATAGCCTAGCCAAGGGTCTTGATATTCGATTGGGGCACAG

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 7
gtaggactttggttcctgatatcagctacaattgccaatattttgctcatgatgtactcatgctagtttgattgctatgtctcatgttcgtactgtgctgtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG
       | |    |   |  | ||||    ||     | | || ||  |||  ||||| | ||  | | | |  | | |   ||     | |||   |||   | |||||||||||||| |||||||| |||||||| ||||| ||||| ||    || ||  ||||||  || || || || || ||||| ||  | || |||||
-------tcttaaccaacaagtaagct-tttttttttctttctttcttttgaattactcttccttctataaattat-tattatatcactcttctggtgtgtatttacagGAGGTACTGCTCCCTGGTGGTCATGGTCTTATGGTCCGTGGCTACTTGCCTGTTGTAAATAGCCTAGCCAAGGGTCTTGATATTCGATTGGGGCACAG

upper sequence: LOC_Os04g53190.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaggactttggttcctgatatcagctacaattgccaatattttgctcatgatgtactcatgc-tagtttgattgctatgtctcatgttcg-tactgtgctgtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG
                     | || |||| ||     | |  |  | | ||  |  |  ||  |||  || ||  |   | |   |||    |||  |      |||||||||| | || | |||||||| || ||||| |||||| | || |||||||| || || ||||||||||| ||||| || ||||| ||  | ||||||||
--------------------gttagttaca-ttctttctctcgtagttaagagttttttttgtatagactgcttcttgaatttttggtttaacactccgagaaatgtgcagGAGGAATTGTTGCCTGGTGGACACGGTCTTATGGTTAGAGGGTATCGTCCTGTCATCAATACTCTGGCGAAAGGTCTTGATATCCGAGTAGGCCACAG

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|33795011|gb|CF323384.1|CF323384
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|88346818|gb|CI657369.1|CI657369
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|58691687|gb|CK080374.1|CK080374
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|88349768|gb|CI632903.1|CI632903
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|29612733|gb|CB617746.1|CB617746
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|58611141|gb|CK038853.1|CK038853
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|58663716|gb|CK052402.1|CK052402
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|58592813|gb|CF991121.1|CF991121
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|58588158|gb|CF986466.1|CF986466
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|33797085|gb|CF324408.1|CF324408
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
EST: gi|58683985|gb|CK072672.1|CK072672
EST:     GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAG                         GAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA
genomic: GTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCA

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: 64 (upstream exon), 65 (downstream exon)
Score: 49

AGAAGGGATTGCTCATGATGTTCTTCAGTGGTATTTGTGCCGCATGGAAGGTTGGTTTGCTACTGATGCGGACGCAATCTCTCTTCAGGGTTGGGACCAGgtaggacttt ... gtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcatgctagtttgattgctatgtctcatgttcgtactgtgctgtgggtgcagGAGGTACTGCTTCCTGGTGGCCATGGTCTCATGGTTCGTGGATATCGTCCAGTAATAAATACTCTGGCAAAAGGCCTAGATATACGCCTTGGCCACAG
           gtttgat  putative branch site (score: 49)
            tttgatt  TA-rich tract