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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG

Basic information

species Oryza sativa
transcript LOC_Os12g34860.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AC211349.4_FGT001 (Zea mays), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                     | |     |   |  | |||  |||| |||  ||  |   |   | ||| || |    | |    |  |  | | |||||||   |  |  |  |||||||||||||||||||||||| |||||||| |||| ||||| || ||||||||||| |||||||| |||||||||| |||||| |||||  ||||||||||||| |
-------------------------------------------------------------------------------------tggcttcttccctgatatttgcttcaaatt--cgtgcctttacggaaacggtatgtagt-agttttgggcctctggctgacctatatatgttctttgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAACGACACATATTATGTTGATGGTCAAACAGTCTTAAGGTGTCATACCAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G078756_T02 (Zea mays), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtg-tactttgaaccatatgattattg-ctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                        ||  || || | | | || ||||||||  || ||| |||  |  ||| || ||  | | |   | || |   || ||||||   |  |  |  | |||||||||||||||||||||| |||||||| |||| ||||| || |||||||||||||||||||| |||||||||| |||||| |||||  ||||||||||||| |
---------------------------------------------------------------------------------------atgtgct-gtgtgtttgttcttcagatt--cgtacatcttcagggacaatggtatgtggtagtttttggtctctggctgacctataaatgttcttcgctgcagAATTTTGATGATGTCTTGGTCCCTTCTGACCATGTAAGCCGGAGTTACAATGACACATATTATGTTGATGATCAAACAGTCTTAAGGTGTCATACCAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G58140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgt-gtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                              |   |||    |  |||  ||  |      || |  ||| || |    |||   | || |||| |||  ||               | |   ||||| ||||||||||| || ||||||||||||||||| ||  | |||   |||||||| |||||||| ||  | |||||||| ||| | |||||||| || |
---------------------------------------------------------------------------------------------gtacgttttcagtactcaagtttgcatctttctagaagtatcacttggtttt---caatgtgatcattattggtttt----------tggtaccagAACTTTGATGATGTGCTAGTCCCTGCTGATCATGTAAGCAGAAGTCTTAATGACACGTACTATGTAGACTCACAAACTGTTTTGAGATGTCATACGAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                             ||     ||   |||| ||       |||  |||   |||       |||    ||   | || |   |    |||||  |||  |   ||  |    || |||  |||||||||||||||||||  |||| ||| |||||||  | ||| ||||||||||||| ||||||||  ||||| |||||||||||||| ||||||| ||||| |
-----------------------------------------------------------------------------atcctatttatagcacatgagaga--tttggtcaatgtctg------cttccaaaattct-tattcatatttctatga--attcttatgccagaaaatatacttcttgcagAATTTTGATGATGTTTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGATCCTCAAACTGTCTTGAGGTGTCACACCAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgatt----attgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                           |  |  |||        |  || | | |  ||   | ||   |     | | | | ||||||   |    |||  |   ||  |  |  | |||  |||||||||||||||||||| |||| ||| |||||||  | ||| ||||||||||||| ||||||||  ||||  |||||||||||||| |||| || || || |
-------------------------------------------------------------------------------------------atcttatttataaggcatgggagttttggtcaatgtctgcttcca-aaattcttatccatatttctgtgaattcttatgccagaaattttacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgacccca-aggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                                                         |  | | ||| |      |  |  ||    ||     ||  |   ||  |  | |  |   |   || | | || |  ||| |     | |||  |||||||||||||||||||| |||| ||| ||||||| || ||| | ||||||||||| ||||||||  ||||  | |||||||||||| |||| || || || |
-----------------------------------------------------------------------------------------gatcctatttataaggcatggaagtttggtcaatgtctgcttccaagattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACGTCAGTAGAAGTTACAATGATACATACTACATTGACTCCCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 1
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                        |  | |  |   |||  | || ||| | |   ||          |||  ||   | |||||    ||               || ||       ||||| |  |  || ||  || ||| | |||  |||||||||||||||||||| |||| ||| |||||||  | ||| ||||||||||||| ||||||||  ||||  |||||||||||||| |||| || || || |
-------------------------------------------------------atcctatttataaggcatgggagttttggtcaatg----------tctgcttccaaaattcttatcca---------------tatttc------tatgaattcttatg-ccagaaagtc-tacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGGG

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0011g01390.t01 (Vitis vinifera), 3'ss of exon 2
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgct-gcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGT--CATACCAGCG-
                                                                                    ||| |  | |  | |||   |||      ||  |  |    ||   ||    || |||||        | ||   |||       | | |      | || |||||||||| |||||||| |||| |||||||||||||||||   ||||| | ||  ||   | |  |     |    | |||| ||  | ||   |||||    | 
-----------------------------------------------------------------------------------ttttctttattgatgtttgacttt-----gtttgcatattgattagatagttttgaacttttgtaagagttatccatgc-atttttatgattgaatctacttgcagAATTTTTATGATGTCTTGGTTCCTGCTGATCATGTGAGCATGAGTTGCCATTGCA---AGTGGGCATCAGACAGAGCTGTTTTAGGATGGGGCATACTCATGA

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 3
gtatgagttagcagttggcctgatgtgttcaactgcttattccttcccttttgtgctgatttccactgggctagtgaatttcgctttgtgcacttgtttttctttttttcagattctcgcacaccttgtgtaacagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                                                        |  | |  |   |||  | || ||| | ||| ||          |||  ||   | |||||    ||               || ||       ||||| |  |  || ||  || ||| | |||  |||||||||||||||||||| |||| |||  |||||| || ||| ||||||||||||| ||||||||  | ||  |||||||||||||| |||| || || |  |
-------------------------------------------------------atcctatttataaggcatgggagttttggtttatg----------tctgcttccaaaattcttatcca---------------tatttc------tatgaattcttatg-ccagaaagtc-tacttcttgcagAATTTTGATGATGTCTTGGTTCCTCTTGATCACGTCAGTAGGAGTTACAATGATACATACTACATCGACTCTCAAACTGTCTTGAGGTGCCACACTACTG

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|29629251|gb|CB634262.1|CB634262
EST:     GGAACTTTAACAAGTTCGATGACCTCTGCCCTCTTGTTTCTATCAAGCAG                         AATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAAT
genomic: GGAACTTTAACAAGTTCGATGACCTCTGCCCTCTTGTTTCTATCAAGCAGgtatgagtta ... cttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAAT
EST: gi|29662500|gb|CB658775.1|CB658775
EST:     GGAACTTTAACAAGTTCGATGACCTCTGCCCTCTTGTTTCTATCAAGCAG                         AATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAAT
genomic: GGAACTTTAACAAGTTCGATGACCTCTGCCCTCTTGTTTCTATCAAGCAGgtatgagtta ... cttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtactttgaaccatatgattattgctgaccccaaggtcatgcttgctgcagAATTTTGATGATGTCCTGGTCCCTGCTGATCATGTGAGTCGGAGTTACAATGACACATACTATGTTGATGCTCAAACTGTCTTGCGGTGTCATACCAGCG
                          tgctgac  putative branch site (score: 2)
                atatgattatt  TA-rich tract