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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcaccaggattatatagcttgtcagactgcatgtactttatgaaatattctcaatttctttacattccttattgatttgggtgtgtag

Basic information

species Oryza sativa
transcript LOC_Os01g09120.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09120.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G176506_T07 (Zea mays), 5'ss of exon 4
GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcaccaggattatatagcttgtcagactgcatgtactttatgaaatattctcaatttctttacattccttattgatttgggtgtgtag---------------------------
||||||||||||||||||| |||||||||||||||| | |||| ||||| || ||||||||  |||||||||||||  |||||||  |||||||||||||||||||  |||  |||   ||  || | |||  || |  || |  |  ||   |    | ||||  ||  ||                           
GTTACTCAAGAGAAGAAATATTGGGCTGTAACTGCAAAGTCTTAAATGGGCCAGGCACTAGCTTGGAGGTTTTAGAGGAGgtgcgggccaggattatatagcttgtatgaccacat--tctccataatatag-cttaccttttaaaatttatattcaaaattggacgtacagataaatcagcatatttgttctgagcag

upper sequence: LOC_Os01g09120.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G176506_T04 (Zea mays), 5'ss of exon 4
GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcaccaggattatatagcttgtcagactgcatgtactttatgaaatattctcaatttctttacattccttattgatttgggtgtgtag
||||||||||||||||||| |||||||||||||||| | |||| ||||| || ||||||||  |||||||||||||  |||||||  |||||||||||||||||||  |||  |||   ||  || | |||  || |  || |  |  ||   |    | ||||  ||  ||
GTTACTCAAGAGAAGAAATATTGGGCTGTAACTGCAAAGTCTTAAATGGGCCAGGCACTAGCTTGGAGGTTTTAGAGGAGgtgcgggccaggattatatagcttgtatgaccacat--tctccataatatag-cttaccttttaaaatttatattcaaaattggacgtacag

upper sequence: LOC_Os01g09120.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G176506_T02 (Zea mays), 5'ss of exon 4
GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcaccaggattatatagcttgtcagactgcatgtactttatgaaatattctcaatttctttacattccttattgatttgggtgtgtag---------------------------
    ||||||||||||||| |||||||||||||||| | |||| ||||| || ||||||||  |||||||||||||  |||||||  |||||||||||||||||||  |||  |||   ||  || | |||  || |  || |  |  ||   |    | ||||  ||  ||                           
----CTCAAGAGAAGAAATATTGGGCTGTAACTGCAAAGTCTTAAATGGGCCAGGCACTAGCTTGGAGGTTTTAGAGGAGGTGCGGGCCAGGATTATATAGCTTgtatgaccacat--tctccataatatag-cttaccttttaaaatttatattcaaaattggacgtacagataaatcagcatatttgttctgagcag

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|29660689|gb|CB656964.1|CB656964
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29660992|gb|CB657267.1|CB657267
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|88221282|gb|CI221238.1|CI221238
EST:     GGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: GGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|86505958|gb|CI148591.1|CI148591
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29657673|gb|CB653948.1|CB653948
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29680769|gb|CB677044.1|CB677044
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|88966127|gb|CI013003.1|CI013003
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29662742|gb|CB659017.1|CB659017
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|86527492|gb|CI167698.1|CI167698
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|88461305|gb|CI547485.1|CI547485
EST:     GTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: GTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|87027196|gb|CI278228.1|CI278228
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|31818552|gb|CD645551.1|CD645551
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTGGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29640574|gb|CB645583.1|CB645583
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29655805|gb|CB652080.1|CB652080
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTATTAAAA
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|14571448|gb|BI118816.1|BI118816
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|38474285|gb|CF958417.1|CF958417
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATNAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|88228766|gb|CI228246.1|CI228246
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29660961|gb|CB657236.1|CB657236
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC
EST: gi|29638115|gb|CB643124.1|CB643124
EST:     ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAG                         ATAAATCAACATATTTGTTTTGAGCAAGCTTGCACGGTTCATCTACTAAAC
genomic: ACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcacca ... gggtgtgtagATAAATCAACATATTTGTTCTGAGCAAGCTTGCACGGTTCATCTACTAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTACTCAAGAGAAGAAATCTTGGGCTGTAACTGCAGATTCTTGAATGGTCCTGGCACTAGTGTGGAGGTTTTAGAACAGgtgcgcaccaggattatatagcttgtcagactgcatgtactttatgaaatattctcaatttctttacattccttattgatttgggtgtgtag

- - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG