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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccccaccactagcaaccacatcgatcacaggcattttctcatcgagacgtgctgaattccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC

Basic information

species Oryza sativa
transcript LOC_Os01g14440.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G871347_T02 (Zea mays), 3'ss of exon 3
---------------------------------------gtaagaccccaccactagcaaccacatcgatcacaggcattttctcatcgagacgtgctgaattc-caaatcgttt-tggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
                                        |    |       ||   | |    |  ||      | || | || |     | | ||   ||| || || |    || |   | |||||||||||| || ||||| ||| | |||||||| ||||||||||| ||||| ||||| || || || || |||||||| ||||||||||||| ||||||||
gtaaggaggagtttttgtttttcctttctctttctttctttctttctttctttcttctatctttctttattttttcctttctttctttctttctttctttcttctcatatggaagatgatcgtgggcagATCGCCGACGGCTGCCAGTGGCGCAAGTACGGGCAGAAGATGGCCAAGGGCAACCCATGCCCGCGAGCCTACTACCGGTGCACCATGGCCAACGGCTGCC

upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA07G39250.1 (Glycine max), 3'ss of exon 4
gtaagaccccaccactagcaaccacatcgatcacaggcattttctcatcgagacgtgctg-aattccaaatcgttt-tggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
             |     |   | || |||       |     | ||  | |  |  |  |  || || |  ||  |  ||   | ||||||   ||||||||||||||| | || || || || |||||||| ||||||||||||||||| || || |||||| | |||||||||||    || ||||
-----------gtagattaatttatatagattgtca-tagcaagtgatgaatatatagtatagctctaacttattaattattatttccagATCAGTGATGGGTGCCAATGGCGAAAATATGGACAAAAGATGGCTAAGGGAAACCCTTGTCCTCGAGCATACTACAGATGCACCATGGCAGTTGGTTGCC

upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G01490.1 (Glycine max), 3'ss of exon 4
gtaagaccccaccactagcaaccacatcgatcacaggcattttctcatcgagacgtgctg-aattccaaatcgttt--tggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
||| ||  | | || |   ||  | |  ||| |     |     | ||  | |  |  |  |  || || |   ||  |  ||   | ||||||   ||||||||||||||| | || || || || |||||||| ||||||||||||||||| || || |||||| | ||||| |||||    |||||||
gtatgaatcaatcattctgaattata--gatta-gcatagcaagtgatgaatatatagtatagctctaacttaattattatttatttccagATCAGTGATGGGTGCCAATGGCGAAAATATGGACAAAAGATGGCTAAGGGAAACCCTTGTCCTCGAGCATACTACAGATGCACTATGGCAGTTGGCTGCC

upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G62300.1 (Arabidopsis thaliana), 3'ss of exon 4
------------gtaagaccccaccactagcaa--ccacatcgatcacaggcattttctcatcgagacgtgctgaattccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
             | |||  | |  |||   ||  | | ||  |  | |  |  | |    | ||||     |   ||   | |  || || |||  |  ||||   |||||| || |||||||| || || || ||||||||||| || || || |||||||| || || || ||||||||||| |||||||| ||||| |
gtaagttgatttattagatactaatacttataagactatataaaaaataaactatgtgctttagagattaattatctttgtact--ttatgtttctat--agATAAGCGATGGATGTCAATGGAGAAAATATGGCCAGAAGATGGCCAAAGGGAATCCTTGTCCGCGGGCATATTACCGCTGCACGATGGCCACGGGCTGTC

upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv10s0116g01200.t01 (Vitis vinifera), 3'ss of exon 4
gtaagaccccaccactagcaaccaca---tcgatcacaggcatt-----ttctcatcgagacgtgctgaattccaaatcgt----tttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
||||||  |||  | ||        |   || |  | |  |  |     || |  |||  ||    || |||   | |  |    | ||  |   |||||||| | ||||| ||||||||| | ||||| || ||||| ||||||||||| ||||| || || || || |||||||| || ||||||||    |||||||
gtaagaatccaataataatgtttgaaaattcaactagaacccctctgatttgtagtcgtcacagtgtggattgggattaatcgaatatgtgtaactgcagATCACTGATGGATGCCAATGGCGCAAGTATGGGCAGAAAATGGCGAAGGGGAACCCATGCCCGCGAGCCTACTACCGATGTACCATGGCAGTTGGCTGCC

upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S158_166V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------gta-agaccccaccactagcaaccacatcga---tcacaggcattttctcatcgagacgtgctga-attccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
                                         ||  |||   |  | |   |   |   | ||   |  |  || |||  ||      | |   | | |     |||||||||       | |||||   ||| || ||||| ||| |||||||||||||||||||||| || || || || ||||| || || |||||||| |||||  | ||  | || ||||
gtacgttctcattttgtttgtgggatccttacctgcaacatgtgcagagttcggcgcctacttgcgtgttgacgcttgccagcgtttgttcggttctatgaagtaacaccatgaatcgtttt-------ttcagATGAACGACGGATGCCAGTGGCGGAAGTACGGTCAGAAGATGGCTAAAGGGAATCCCTGTCCTCGTGCATACTACCGTTGCACTGTTGCGCCTGGGTGCC

upper sequence: LOC_Os01g14440.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S47_251V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------gtaagaccccaccactagcaaccacatcgatcacaggcattttctcatcgagacgtgctgaattccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
                                          | | |   || |||  |   |        |||  |  |   | | |||| | |        |  ||    | |||   |   |  |||||   || || ||||| |||||||| || ||||||||||||||||| || ||||| ||||| || || |||||||| |||||| | ||  | ||||| |
gtacgttcctgtccttttcatagaacccttctctacacgcttttaaaattcagcaccggattcagtgcttttcatcgttaaggtttaatcgggtcccatgatctcacatgatgatttatctgt-tttagATCAATGACGGATGCCAGTGGAGGAAATATGGTCAGAAGATGGCGAAAGGGAACCCCTGTCCTCGTGCATACTACCGATGCACCGTTGCGCCGGGCTGTC

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: 44 (upstream exon), 69 (downstream exon)
Score: 5

CGCCGCCGGCGCGGCGGGCAAGAGCCATGATCAGCAAGCCCAGGATGCCAACATGAGGAAGGCCCGCGTCTCCGTTCGCGCGCGATCCGAAGCGCCAATCgtaagacccc ... ttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggcattttctcatcgagacgtgctgaattccaaatcgttttggttccgtgcagATCGCCGATGGGTGCCAATGGAGGAAGTACGGTCAGAAGATGGCGAAGGGAAACCCTTGTCCACGCGCGTACTACCGCTGCACCATGGCCACCGGCTGCC
     attttct  TA-rich tract