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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATACAGAAGTAATCATCAGGGACTACTTTCATCTTTGGACGACAGCATAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatcattccttttgttgcacatcacagtgtccatccaagggatttgcagaattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcag

Basic information

species Oryza sativa
transcript LOC_Os04g51400.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51400.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G140924_T01 (Zea mays), 5'ss of exon 3
AAGATACAGAAGTAATCATCAGGGACTACTTTCATCTTTGGACGACAGCATAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatcattccttttgttgcacatcacagtgtccatccaagggatttgcagaattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcag
 |||||||||||    | ||||| |   ||||| ||  ||||||||||| | |||||| |||||||||||| ||||||  ||| ||  |||| |||||||||||    |||||  ||| |  |||  |||| |   | | | | |     |||||  ||||   | |   || |    | |||   | | |    || | |                                               
GAGATACAGAAGCGGGCTTCAGGAAGGGCTTTCGTCCCTGGACGACAGCGTGGAGGATTCAAATGGGTACTTGCGCTTTGATACGGGTGGAATTGAAGAGgtaaga--cattctatttctgtcactgcacaatagtcgtgctaagt-ccagcagagctatg-aagagaatgcaaa---tcgtatgattacattg-tgcactgcag-------------------------------------------

upper sequence: LOC_Os04g51400.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G053909_T01 (Zea mays), 5'ss of exon 3
AAGATACAGAAGTAATCATCAGGGACTACTTTCATCTTTGGACGACAGCATAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatcattccttttgttgcacatcacagtgtccatccaagggatttgcagaattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcag
 |||||||||||  ||| |||||||   ||||| ||  ||||||||||||| |||||| ||||||| |||| ||||||  || |||  || | ||||||||||| |  |  ||  ||| |  |||  ||||      || | | |     ||||| || |   |    ||  |       || |||          || | ||||  | |  ||||  ||   |||     |||||| ||| | ||||
TAGATACAGAAGCGATCTTCAGGGAGAGCTTTCGTCCCTGGACGACAGCATGGAGGATCCAAATGGATACTTGCGCTTTGATGTGGGCGGGATTGAAGAGgtaagg--cggtctatttctgtcactacacaacagtaatgctaagt-ccagcagagtttt--tcttttgattt--tccaagtccagca--------gagtcatgtagagt--atttctgt---cac-----tatattgtgtgttgcag
















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|29676639|gb|CB672914.1|CB672914
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|58691609|gb|CK080296.1|CK080296
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|89196993|gb|CI021833.1|CI021833
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGGAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29666124|gb|CB662399.1|CB662399
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29671277|gb|CB667552.1|CB667552
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29666123|gb|CB662398.1|CB662398
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29676637|gb|CB672912.1|CB672912
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|29626982|gb|CB631993.1|CB631993
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|86841641|gb|CI337348.1|CI337348
EST:     GGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: GGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
EST: gi|9865894|gb|AU101644.1|AU101644
EST:     TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAG                         CTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC
genomic: TAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatca ... tgtctcgcagCTTGAGAACTACTTCATATTCAATGATCGGTACAGAGGGATGAGAATGGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATACAGAAGTAATCATCAGGGACTACTTTCATCTTTGGACGACAGCATAGAGGATGCAAATGGGTACTGGCGCTTCAATATGGAAGGAAGTGAAGAGgtaaagatcattccttttgttgcacatcacagtgtccatccaagggatttgcagaattatgtgcgggcgagctagctttggtacagtgaaaaaactgaattatgtgcaatccattttggtgctcacatagttatattctgtctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA