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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc...

Basic information

species Oryza sativa
transcript LOC_Os01g67250.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G421829_T01 (Zea mays), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc-
||||||||||| |||||||||||||||||||| || || || ||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||| |||||||||||   |||||    |         |||  ||||| |||||          |||    ||  ||  | ||  |||  ||| | ||  ||||  ||  
GCCAAGAAGGGCCCCCTCGGGACCATATGGATTGCCGCACACTTGGAGCGGAAGCTGCGCAAGAACCAGGTCGCGGACACGGACATCGGCGTCTCAGTAGgtgggtggccttgcttacgctttcagcaatttgatttcg-atctagggtttgcgctttactgttaggtctgtgcgagttgtggcttgacctgtaggatggt

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G093119_T01 (Zea mays), 5'ss of exon 2
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc---------
||||| ||||| |||||||||||||||||||| || ||||| ||||||||||||||||| ||||| ||||||||||| ||||| |||||||||||||||||||||||   |||||      |||||||    |  || |  |  | |     |||||||  | |    |   |  |||   | ||| || |||||  ||          
GCCAAAAAGGGTCCCCTCGGGACCATATGGATTGCCGCGCACTTGGAGCGGAAGCTGCGCAAGAACCAGGTCGCGGACACGGACATCGGCGTCTCCGTAGgtgggtggccttgct------caagcttccaacaatttgctttcaatctaggtttttttgctctactgttaggtctgt---gacctgacccgtaggatggtaaagtgtt

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA18G48020.1 (Glycine max), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactacc------atttttttttgttt-ctgttcgagcatgttagggcctcacacgtagactgc
|||||||| ||||| || ||||| |||||||| || |||||||||||| ||||||| |||||||| ||||| || ||||| || || |||||||||||||||| ||  || |  |||| | |  |||||||  |||  |  | || | |        |||| |||||||  ||    | | |  ||| ||   ||      |     
GCCAAGAAAGGGCCACTTGGGACTATATGGATAGCTGCGCATTTGGAGAGGAAGCTCCGGAAGAACCAGGTGGCAGATACCGACATTGGCGTCTCCGTAGgtgtgt--ttgttttgttccgc--gctttttaatttgagtttttaatgcgtggagagttttgttttgttagctagcagtgtaatttatggttgcaattactgtt---

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA09G38310.1 (Glycine max), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc----
|||||||| ||||| || ||||| |||||||| || |||||||||||| ||||||| || ||||| ||||| |||||||| || || |||||||||||||||| ||    ||||| | |  |  ||| |||  |||     | || | |       |||   || |||| |       | |    |   |     | |      
GCCAAGAAAGGGCCACTTGGGACTATATGGATAGCTGCGCATTTGGAGAGGAAGCTCCGCAAGAACCAGGTGGCGGATACCGACATTGGCGTCTCCGTAGgtgcgt----ttgctttgttccctgctctttaatttggatttttaatgcgtggagatttgtgttttgttagttagcagtggaatttatgattgcaattaatgtt

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G16270.1 (Arabidopsis thaliana), 5'ss of exon 2
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttct-----tttcggatctactaccatttttttttgtttct----gttcgagcatgttagggcctcacacgtagactgc------------------------------------------------------------------
|| ||||| ||||| || ||||| |||||||| || || ||||||||| ||||||| || |||||||||||||| ||||| ||||| || |||||||| |||| || ||||||||   |       || | |        |  |  ||   |  || ||  || || |       ||| |   | | ||  |  ||   | |   | |                                                                   
GCTAAGAAAGGGCCACTTGGGACAATATGGATTGCTGCCCATTTGGAGAGGAAGCTTCGAAAGAATCAGGTCGCTGATACTGATATTGGAGTCTCCGTTGgtgagt-attttgctaccttttgcttttgtgtacaatacctctgattcaggtctcagttcgttgtgctcactagggttagcagaagctaaagtttccttctttttcagttgttatgtggctaaacaagttcatctaaaatatttcctaatataactaatttctttttctgagcag

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv00s0220g00080.t01 (Vitis vinifera), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatg-ttagggcctcacacgtagactgc----------
|||||||| ||||| || |||||||||||||| ||||||||||||||| ||||||| |||||||| ||||| || ||||| ||||| |||||||| ||||||  ||    |   || ||        | |||  || | ||   | | |   |||  |    ||    |  |||    || ||      | ||| |  | |          
GCCAAGAAAGGGCCGCTTGGGACCATATGGATAGCGGCGCATTTGGAGAGGAAGCTCCGGAAGAACCAGGTTGCTGATACTGATATTGGCGTCTCAGTAGgtcagt----tcagtgctt------tctgtttggttcctgagaaagt-ctgctttcctcgacttggaattaagcccaattgggaagcttctcgttggtttcatttattttc

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S77_167V6.2 (Physcomitrella patens), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatct-----actaccatttttttttgtttctgttcgag-catgttagggcctcacacgtagactgc
|| || ||||| || || |||||||||||||| || || ||||||||||| ||| ||||||||||||||||| |||| ||  ||||  |||| ||||| |||  ||| |  | ||   ||          |      || |  |     |   |  | ||| |  ||| ||  | | | ||  |  ||   |||    |  |    
GCGAAAAAGGGTCCGCTGGGGACCATATGGATAGCTGCTCATTTGGAGCGCAAGTTGCGGAAGAATCAGGTCACGGAAACAAATATTAGCGTATCCGTCGgtaagtg-tgctcctaactcgtttaaggcatggaaaccgaacgttggagagagcagtctttgtaagttactcctggtgacacatctggaagtca-gtttgca----

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ11860 (Selaginella moellendorffii), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc
||||||||||| || || || ||||||||||| || || ||| ||||||||||||| |||||||| || ||  | || ||  | ||||| || || || |||  || |       | |  |  |  || |||| || | ||   |     | |||||| | ||  | ||| ||                           
GCCAAGAAGGGACCGCTGGGTACCATATGGATTGCTGCTCATCTGGAGCGGAAGCTCCGGAAGAACCAAGTTACCGAGACCAACATCGGTGTGTCTGTGGgtaagtcac------gatctaggatgttgtttcgttgctga---aaagagagttttttcttttctttttctag---------------------------

upper sequence: LOC_Os01g67250.2 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ13427 (Selaginella moellendorffii), 5'ss of exon 1
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc
||||||||||| || || || ||||||||||| || || ||| ||||||||||||| |||||||| || ||  | || ||  | ||||| || || || |||  || |       | |  |  |  || |||| || | ||      |   |||| |||| ||| | ||| ||                           
GCCAAGAAGGGACCGCTGGGTACCATATGGATTGCTGCTCATCTGGAGCGGAAGCTCCGGAAGAACCAAGTTACCGAGACCAACATCGGTGTGTCTGTGGgtaagtcac------gatctaggatgttgtttcgttgctgaaaagagagttttttctttttttttttttctag---------------------------

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|95101281|gb|CI693024.1|CI693024
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88576761|gb|CI673286.1|CI673286
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAC                         ATTCAATTATATTCCCTGAAGTTCCGATTGCANTTCGATCATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88583301|gb|CI700772.1|CI700772
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|29630217|gb|CB635226.1|CB635226
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88429094|gb|CI689974.1|CI689974
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCACGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88588063|gb|CI705856.1|CI705856
EST:     GAAGCTGCGGAACAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|88381570|gb|CI682231.1|CI682231
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
EST: gi|29678404|gb|CB674679.1|CB674679
EST:     GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAG                         ATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC
genomic: GAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgatt ... tttcctgcagATTCAATTATATTCCCTGAAGTTCCGATTGCACTTCGATTATCAAGCCATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAGAAGGGGCCCCTCGGGACCATATGGATCGCGGCGCATTTGGAGCGGAAGCTGCGGAAGAATCAGGTCGCGGATACGGATATCGGCGTCTCCGTAGgtgggtgattttgctgtttcacaagcttttttcttttcggatctactaccatttttttttgtttctgttcgagcatgttagggcctcacacgtagactgc

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA