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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatacttcatttaatgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG

Basic information

species Oryza sativa
transcript LOC_Os07g19560.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AC185415.3_FGT005 (Zea mays), 3'ss of exon 4
taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatacttcatttaa-------tgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
     ||| ||||     |  | || |    |  ||  || ||| |  |        |        || || ||||||||    |  ||        ||| ||||||||| |||||||| || ||||| ||||| |  ||||||||||| ||||||||| ||||||| |||  |||||||||||       
-----tga-ctgccaccctctatgc-ctgcagcaatttttatacttcattagtcaaaacttgctgtctgatatgatgatatgaaacctagcttcatttgtgttccagGTGCGGCAACATCAACTGGGCTAAGCGTACCAAATGTAATATATGTAACACCTCCAAGCCTGGTACCAATGAAGGTG-------

upper sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AC233865.1_FGT006 (Zea mays), 3'ss of exon 4
taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccg-cttatgtgatgata----cttcatttaatgttt-tccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
    || | ||||     |  | |    |  |  ||  || | | |  |  | | | |     | | ||||| ||||||||    |   | || || | | ||||||||||||||||| || ||||| |||||||  ||||||||||| ||||||||| ||||||| |||  ||||||||||||||| ||
----tttaactgccaccctctatgtctta-agcaatttttatgcttcat-tagtataaacttgctgtcttatatgatgatatgaacccaacttcatttgtgtccagGTGTGGCAACATCAACTGGGCTAAGCGGACCAAATGTAATATATGTAACACCTCCAAGCCTGGTACCAATGAAGGTGGTGTGAG

upper sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA12G03260.1 (Glycine max), 3'ss of exon 3
taaattgatctgca-gtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatact-tcatttaatgttttcc------agGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
        | ||||  | ||     |||  | ||| |   || |   | |  ||  | | ||       ||||   |||   | |||| |  | ||||        |||||||| || || ||||||||||||||||  ||||| |||||||| ||||| |  ||||| || || ||||| |||||||| ||
--------tttgcacatcatgtgtacacttttgttgtttatgcaggatttttaaaataaaaatttaatgtatgaattgactttctcatgtttttttttttttgcttagGTGTGGGAATATCAATTGGGCAAAGCGGACTAAATGCAATATCTGCAACACAAATAAGCCTGGGCATAATGAGGGTGGTGTAAG

upper sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G50300.1 (Arabidopsis thaliana), 3'ss of exon 4
taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgtta--taaaaccgcttatgtgatgatacttcatttaatg--ttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
||   | || ||   |   |  |||  ||     | || || ||  |||  ||||| |  |   |    | |||   |  | |||  |    |   | || ||||||||||||  | || ||||| || ||  | |||||||||||||| |||||||  || || ||||| |||||||||||||| ||
tatgct-atgtgtcatcg-agtagcttaactaaga-ggctgcactgtgtg-aatgtgagttcttatgcataatgcactttttctttttgcgctaattctttcagGTGTGGCAATGTCAACTGGGCGAAACGTCTAAAATGTAATATCTGCAACACCAATAAACCTGGTCAGAATGAAGGTGGTGTGAG

upper sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0010g01410.t01 (Vitis vinifera), 3'ss of exon 3
taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatacttcatttaatgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
 || || |||     |  |  ||  |  ||||| |       | |   || | | ||      |   ||   |  |  |  |   | | |  | || ||||||||||||||| || |||||||||||||  || || ||||| || |||||||  ||||| || || |||||||||||||| ||
caatttaatccatgatgttttaaaaaatatggtcaaataaacatcacataaattattgcttttcatattgcttcttccttatgattatgagttgtttcagGTGTGGCAACATTAACTGGGCAAAGCGGACAAAGTGCAATATATGCAACACCAATAAGCCTGGCCATAATGAAGGTGGTGTGAG

upper sequence: LOC_Os07g19560.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S148_65V6.2 (Physcomitrella patens), 3'ss of exon 3
----taaattgatctgcagtaataaaagcacaatggttatggttgtaccttgtacaatgttataaaaccgcttatgtgatgatacttcatttaatgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
        || |   ||| |       |   || | || |   |  | |  | | | | | |   | ||||  |  |     || ||  | |  | |  | |||||||||||||||||||||||||||||| |  |||||||| ||||| |||||  |||| || |||  ||||||||| ||||  ||
ttcacgtcttcaaaggcattctcttgtgttgaaggatttt--ctagatcc-gcatagtttaagggatccgccaagttttccttattttttatggt-tcatgcagGTGTGGCAACATAAATTGGGCAAAGCGCACAAAATGTAACATCTGCAACACTGCCAAACCTGGTTTCAATGAAGGCGGTGCCAG

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|29637898|gb|CB642907.1|CB642907
EST:     GTTGGTGGTCCTCCTGGACTGTTTGGTCCAAATGATTGGCCTTGCCCAAT                         GTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACAC
genomic: GTTGGTGGTCCTCCTGGACTGTTTGGTCCAAATGATTGGCCTTGCCCAATgtacgaacac ... tgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacaatgttataaaaccgcttatgtgatgatacttcatttaatgttttccagGTGTGGCAACATAAATTGGGCAAAGCGGATGAAATGTAATATCTGTAACACCACCAAGCCAGGTCACAATGAAGGTGGTGTTAG
                                       atttaat  putative branch site (score: 4)
                                             tgttttcc  CT-rich tract
                                    ttcatttaatgtttt  TA-rich tract