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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG

Basic information

species Oryza sativa
transcript LOC_Os12g40830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
ttagtgtatgatggatttgtttta---caagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
 |||| |     |  ||||||| |   |||| |          ||||   |||    ||||||| |  || |||  |    ||  ||  ||  |  |||| |||| || |||||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||      
atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgata-gcctgctcttctcattct--ctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG------

upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G398107_T01 (Zea mays), 3'ss of exon 1
ttagtgtatgatggatttgttttacaagtagtgaattatgtt---ttagtttttcgctttgatatgta--tggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTT-CTAATCATACAGGTAGAG-
| |||   |||  |  |||  || |  ||   |     ||      | || ||||| |  |  || |   | | |      | |||| |   |||| |  || |||| ||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||||||| ||||||||  ||||||||| |||| |||||||  | |  
tgagt---tgactgcgttgcctttcgtgtgacgggcggtgacgagcttgtgtttcgttcggggattttgttagcccaaatagtctgcatggattttgt--ttcagGGGTACGTTGGCAACAAATCGGCCGTCTTCCCCCTGCAGCTCCTCGGCTTTGATGTGGATCCAATAAACTC--TACAGTTTTTCTAACCATACAGTGATACA

upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 2
--ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatat-gtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
  |    | |   || | |  | ||  | ||  | | | |  |    |    | ||| ||  ||    | | || ||| | |||  |  | || ||   | |||| || ||||| || ||||| || ||||| || |||||||| ||||| | |||||| ||||| || || || || |||||||| |||||||||||     
tttcttggcaatttgcagtaatctttgatgttatta-tcaattgcatgcagcttgctatgtaattaccttgact-ttgtggctgtttgctattatt--ctcaggGGTATGTTGGTAATAAATCCGCTGTCTTCCCTCTGCAACTACTGGGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG-----

upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 2
---ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggt-ctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
   |   | |||| | || || |   ||   |  |   || ||| |  || | | | |   | |  | || | |  ||     || || ||  |||    ||||||||| ||||| ||||||||||| |||||||| || ||| |  |||| | |||||||||||| || ||||| ||||| || || ||||||||||      
ctgtctctctatgcttgagttctgcaacttttttttttttgtgtgtgtgtgtgt-gttaccagaaatgtgatgccattttatatgtctattactttc---ttagGGATATGTTGGTAACAAATCAGCTGTCTTTCCTCTTCAATTGTTGGGGTATGATGTGGATCCAATCAACTCTGTACAATTCTCGAATCATACAG------

upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
-----ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
       | |  |  ||    || | |    |||      | |||| || ||  |  | ||  || ||| |  |   ||         ||| | |||    ||||||||| |||||||| ||||| || ||||||||||| || || ||||||| |||||| ||||| || || || |||||||| || ||||| ||||      
aaacaccatttcaacataagcttatgt----agttacatttaatgtgtttgtggta-gattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG------

upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ27991 (Selaginella moellendorffii), 3'ss of exon 1
ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
                                   | |    | | | | || ||    |     || ||    | || |   |  | |  |  |   ||||||||||||| || ||||| || ||||||||| |||| |||||||| || ||||| |||||||| |||||                             
----------------------------------gtaagcgctcaatatctcactggattgcaagtgatcc--cgagctt--ttactctactcgagacagGGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCC----------------------------

upper sequence: LOC_Os12g40830.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29421 (Selaginella moellendorffii), 3'ss of exon 1
ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
                                   | |    | |   | || ||    |     || ||    | || |   |  | |  |  |   ||||||||||||| || ||||| || ||||||||| |||| |||||||| || ||||| |||||||| |||||                             
----------------------------------gtaagcgctcaaaatctcactggattgcaagtgatcc--cgagctt--ttactctactcgagacagGGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCC----------------------------

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|58661072|gb|CK049752.1|CK049752
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         TGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCGTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88580749|gb|CI697698.1|CI697698
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88424098|gb|CI689800.1|CI689800
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     GCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: GCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGGTAGAG
                                            ttttaat  putative branch site (score: 3)
                                cctgcctttttttttt  CT-rich tract
                                      ttttttttttaattta  TA-rich tract