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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg...

Basic information

species Oryza sativa
transcript LOC_Os06g30060.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G341027_T02 (Zea mays), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgg-gccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg
||||||||| |||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| |  ||||||  |   ||    |  | | |   || | |||      |  |||     ||||||      || || |     ||  ||  | | ||    || | |  |
ATCGGGAGCTTGATAAGCCTCATGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTGTACACCATCAACACCGAGGAGTCCAGCATCGGGCTAAAAAACGgtaggatgccatattatctaacggctctcgctctcttctcgtcctaggtgggttggtattctgttggtggaacatgatagttgtt-tgaccatgcgtcagg

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA04G17050.1 (Glycine max), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtg-ggagagggtgtgtgtgtgtgccgcg
|| |||||| |||||||| | || || ||||| |||||| | ||||| ||  | ||||||| |||||||||||| |||||||| || || ||||| |||||| |  || || |  |||      ||     |  |  | ||        |   |    |   || | | | |||   |     || |   |  || ||   
ATTGGGAGCTTGATAAGCTTGACCTCTAAGAGTGAGATCAGATACGAAGGTATTCTCTACAACATCAACACCGAAGAGTCCAGTATTGGCCTCAGAAACGgt-attcttctgctacccacttgttttttttttttttttccaatgaatttcccttaatcctttctgggttttgttcagtttcagtttaatttggttccttt

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G22680.1 (Glycine max), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg---
|| |||||| |||||||| | || || ||||| |||||| | ||||| ||| | ||||||| |||||||||||| |||||||| || || ||||| || ||| |  || || |  |||    | ||  |        ||||      | |   ||||    ||      || ||   |    || ||  |  ||  |      
ATTGGGAGCTTGATAAGCTTGACCTCTAAGAGTGAGATCAGATACGAAGGCATTCTCTACAACATCAACACCGAAGAGTCCAGTATTGGCCTCAGAAATGgt-attcttctgctacccacttttttttcaaggaatttcccttaattcttt-ctgggttttgttctttttcagtttaattttgt-tgctttggtttcagatct

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G11320.2 (Glycine max), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg
|| |||||| |||||||| | || || ||||| |||||| | ||||| ||  | ||||||| |||||||||||| |||||||| || || ||||| ||||||     ||  |   ||    || ||  |        | ||  |   |||   | ||    ||      || ||   |   ||    | ||  | | |  
ATTGGGAGCTTGATAAGCTTGACCTCTAAGAGTGAGATCAGATACGAAGGTATTCTCTACAACATCAACACCGAAGAGTCCAGTATTGGCCTCAGAAACGgtattcttctgctacccacttcttttttcgtatgaatttccctcaatcctttcttggttttgttctttttcagtttaatttggctcctttggtttcagat

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G11300.1 (Glycine max), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccga--gctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg
|| |||||| |||||||| | || || ||||| |||||| | ||||| ||| | ||||||| |||||||||||| |||||||| || || ||||| |||||| |  || || |  |||    |   ||   ||      | ||      |||   ||||    ||      || ||   |   ||| ||  |  ||  |   
ATTGGGAGCTTGATAAGCTTGACCTCTAAGAGTGAGATCAGATACGAAGGCATACTCTACAACATCAACACCGAAGAGTCCAGTATTGGCCTCAGAAACGgt-attcttctgctacccacttgtattttttccatgaatttcccttaatcctttctgggttttgttctttttcagtttaatttggt-tgctttggtttcaga

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv01s0011g02820.t01 (Vitis vinifera), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcc-tcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg
||||||||| |||| ||  | || || || ||||||||| ||||||||||||| ||||||| |||||||||||||||||||||||||||  |  | ||||||        |   ||  | |   || |    | | | |      | |  || ||  |  |  |   || |  ||           | |         |  
ATCGGGAGCTTGATTAGTTTGACATCCAAAAGCGAGATCAGGTACGAGGGCGTTCTCTACAACATCAACACCGAGGAGTCCAGCATCGGATTGCGAAACGgtattttcgttatttcttgcggggtttcgtaactttcgttttattttctttgatttcggtgttttttcgctgcgttttctctcaacttttcccaattggt-

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ22693 (Selaginella moellendorffii), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg
|| || ||| | || |||||||| || |||||||| ||||| ||||||||||| |||||||||||| || ||||| | | || ||||| ||||   |||||| |||||    |     |      |     |    |||  |    | |   |  |  |||    ||  | | |                          
ATTGGAAGCCTCATCAGCCTCACATCCAAGAGCGACATCCGCTACGAGGGCGTGCTCTACACCATCGACGCCGAGAACTGCAACATCGCGCTCCAAAACGgt-aggctatggcgat--gtttcgctagggttggagctcgggagctcacgaatccgtgcgctcttgctttgtttccag----------------------

upper sequence: LOC_Os06g30060.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ13073 (Selaginella moellendorffii), 5'ss of exon 1
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg
|| || ||| | || |||||||| || |||||||| ||||| ||||||||||| |||||||||||| || ||||| | | || ||||| ||||   |||||| |||||    |      |  |||      |       | |   | |  |  |  |  |||     | | |||                          
ATTGGAAGCCTCATCAGCCTCACATCCAAGAGCGACATCCGCTACGAGGGCGTGCTCTACACCATCGACGCCGAGAACTGCAACATCGCGCTCCAAAACGgt-aggctatggcgat---atttctctagggttggagctcgggagctcacgaatccgt-gcgctcttgctttgtttccag--------------------

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|58607778|gb|CK035811.1|CK035811
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGTTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
EST: gi|58672585|gb|CK061271.1|CK061271
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGTTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
EST: gi|29623763|gb|CB628774.1|CB628774
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGTTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
EST: gi|29636795|gb|CB641804.1|CB641804
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
EST: gi|58667348|gb|CK056034.1|CK056034
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGTTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
EST: gi|117231418|gb|CT846842.1|CT846842
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGTTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG
EST: gi|58601474|gb|CK012002.1|CK012002
EST:     CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACG                         TTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGTTCAACAGATTCCAG
genomic: CGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcc ... tgttttgcagTTCGCTCATTTGGAACTGAAGGTCGTAAGAAGGATGGTCAACAGATTCCAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGGGAGCGTGATAAGCCTCACGTCGAAGAGCGAGATCCGGTACGAGGGCGTCCTCTACACCATCAACACCGAGGAGTCCAGCATCGGGCTCAGGAACGgttaggctcctccctcccgagctcttccccctcctcctcccgcctcccctggttgggccgcgtcggcgatctgtgggagagggtgtgtgtgtgtgccgcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG