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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcgccgccgccgcaaatccccagttcactcctcccttccaacacacgcggttaaattaattgaattggctgcagAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC

Basic information

species Oryza sativa
transcript LOC_Os05g38000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G144504_T02 (Zea mays), 3'ss of exon 1
--------------------------------------------gtacgtgcgccgccgccgcaaatccccagttcactcctcccttc-caacacacgcggt---taaattaattgaattggctgc-----------------agAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
                                            |||||| | ||  |||    ||||| |   ||  |     ||   |   ||  || ||   | |     | |   ||  |||                 |||||||||||||||||||||| ||||| | |||||||||||||||||||||||||||||  |||||||||||                             
gcgcggcgtcgtcgccgcggccgacaggcacggaggagcatcaggtacgtacaccagcgcgaataatcctcctatcggtttggtctcggccggacgtgcagtctctcacaccgtcgTCGTGCGTGCCCGCGCGTGAAATCGCCAGAGATGGAGATGATGAAGGAGCGGTTCTCCAAGCTGCTGCTCGGCGAGGACATGTCCGGGAGCGGCAAGGGC-----------------------------

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G144504_T01 (Zea mays), 3'ss of exon 1
gtacgtgcgccgccgccgcaaatccccagttcactcctcccttc-caacacacgcggt---taaattaattgaattggctgc-----------------agAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
|||||| | ||  |||    ||||| |   ||  |     ||   |   ||  || ||   | |     | |   ||  |||                 |||||||||||||||||||||| ||||| | |||||||||||||||||||||||||||||  ||||||||||||||||||||||||||||||||||||||||
gtacgtacaccagcgcgaataatcctcctatcggtttggtctcggccggacgtgcagtctctcacaccgtcgtcgtgcgtgcccgcgcgtgaaatcgccagAGATGGAGATGATGAAGGAGCGGTTCTCCAAGCTGCTGCTCGGCGAGGACATGTCCGGGAGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv13s0019g02710.t01 (Vitis vinifera), 3'ss of exon 1
-------------gtacgtgcgccgccgccgcaaatccc----cagttcactcctcccttccaacacacgcggttaaattaattgaattggctg---cagAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
             ||  | |  | ||||   || |  |     | |||   |  |    |   |    |   ||   |  || | ||     ||   ||||||| ||||||||||||||||||||  |||| ||| |||| || || |||||||| ||    || || || || || || ||  | ||||| || || ||
tcagatagatcctgtttgaggtctgccgattcatactcattagcggttttgtaatttagttatattttctttgtcttaaaaaataaaaaaaatgaaacagAGATTGAGATGATGAAGGAGAGGTTTTCGAAACTGTTGCTTGGTGAAGACATGTCAGGGTCTGGAAAAGGGGTTTGTACAGCTTTGGCCATTTCAAATGC

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S58_274V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------gtacgtgcgccgc-cgccgcaaatccccagttcactcctccc------ttccaacacacgcggttaaattaattgaattggc--tgcagAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
               ||||       |  ||| ||  |  || |||  ||          |  || |   |  |    |||   |    ||    ||||||| |||||||||||||||||||||| || || ||  |||| || || || ||||| || || ||||| || || ||||| ||| | || || || || ||
tgcattactattcgagtgcattttatgatgcatatgtcgtgtacacggctagtgtgatgctgtaatatgtgttgcctgattgtgtcttctgttcttgcagAGGTGGAGATGATGAAGGAGAGGTTTGCAAAACTATTGCTTGGTGAAGATATGTCAGGTGGGGGCAAAGGGGTTTGCACAGCGTTGGCTATATCGAATGC

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S22_225V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------gtacgtgcgccgccgcc----gcaaatccccagttcactcctcccttccaacacacgcggttaaattaattgaattggctgcagAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
                      ||   |     |         ||||||   ||  |||||  ||   |   |     |||      |   ||| |      |||||| ||||||||||||||||| ||||||| ||| ||||||| || ||||||||||| || || |  || || || |  ||||| || || || || || ||
gtttatcctacgtttttgttttgtttttattatgtttttttaagcaaattatcaagtcactgatcgaat--gatggctgcgtc----tcttttgtacatatggcagAGGTGGAGATGATGAAGGAGCGGTTCGCAAAGTTGCTGCTTGGGGAGGACATGTCGGGTGGTGCTAAAGGTGTTTCTACCGCTCTTGCGATTTCGAATGC

upper sequence: LOC_Os05g38000.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S283_2V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------------------------------------------------------gtacgtgcgccgccgccgcaaatcc-ccagttcactcctcccttccaacacacgcgg-ttaaattaattgaattggctg-cagAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
                                                                                                                      || ||  |  | |   |  ||   |  |  |     |  |     |     || || | || ||| | ||   || ||||| ||||||||||||| ||| |||| || ||| ||||||| || ||||||||||| || || | ||| || || |  ||||| || || || || || ||
gttgaaacttgaccttgccacttagttcgtgcgggcctcccaagtagtatgacattgccgttgtatgtgcatgttattctgtgtcaagtttgtttgagaaacacgcgtcaatgctcttgtccgaagatgtcttgatgccattaaattgcgaaaactctgatggattgatggcttcatttcatttacttaaatgacagAGGTGGAGATGATGAAAGAGCGGTTTGCCAAGTTGCTGCTTGGGGAGGACATGTCAGGTGGTGCCAAAGGTGTTTATACCGCTCTGGCGATATCAAATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagttcactcctcccttccaacacacgcggttaaattaattgaattggctgcagAGATGGAGATGATGAAGGAGAGGTTCGCGAAGCTGCTGCTCGGCGAGGACATGTCCGGCGGCGGCAAGGGCGTCTGCACCGCGCTCGCCATCTCCAACGC
                                  aattaat  putative branch site (score: 3)
                               ttaaattaattgaatt  TA-rich tract