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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgattccacttcaatctttgtatattagtacttgagtttgtacgcacaaatgtatggatatttgttgagccaaaaaaagaagtgaggtgctctg...

Basic information

species Oryza sativa
transcript LOC_Os04g52370.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 4
GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgattccacttcaatctttgtatattagtacttgagtttgtacgcacaaatgtatgg-atatttgttgagccaaaaaaagaagtgaggtgctctg----
|| ||||| || || ||||| |||||||| |||||||||||||||||| ||  || | ||||  | |  ||| |||     ||| ||||  |      |||   |  | ||||| |  |          |    || | ||    
GGTACTCGTCTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgctttaacctgaatccct-tgcatt-gtat---ggttagtacttaatttcatatctcacgtgtgttgtgttatgggttctgttttcctgttttggatc

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G044629_T01 (Zea mays), 5'ss of exon 4
GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgattccacttcaatctttgtatattagtacttgagtttgta-cgcacaaatgta-tggatatttgttgagccaaaaaaagaagtgaggtgctctg
|| ||||| || || ||||| |||||||| |||||||||||||||||| ||  || | ||||  ||||| ||||||| | | ||  || | ||||  || | ||  | ||   ||               |  |   | |  
GGTACTCGACTGGGAAGCTCAGATCCTAAGGGATGTTTCAgtaagttgctttaacctgaatccctgtatgttagtacctaacttcatatctcacatgtgcagtgagtgttatgtgttttcttctcctgttttggaaccac--
















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|58674987|gb|CK063674.1|CK063674
EST:     GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCA                         GTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGA
genomic: GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgat ... tgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGA
EST: gi|396941374|gb|HO188583.1|HO188583
EST:     GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCA                         GTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGA
genomic: GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgat ... tgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGA
EST: gi|58611448|gb|CK039160.1|CK039160
EST:     GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCA                         GTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGA
genomic: GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgat ... tgccctttagGTATCGGACTTCCGTCTGGAAAGTCGCTTTTCCAACTCCAAGCTGAACGGA
EST: gi|58676295|gb|CK064982.1|CK064982
EST:     GAGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCA                         GTATCGGACTTCCGTCTGGAAAGTC
genomic: GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgat ... tgccctttagGTATCGGACTTCCGTCTGGAAAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACTCGGCTTGGTAGCTCTGATCCTAAAGGATGTTTCAgtaagttgattccacttcaatctttgtatattagtacttgagtttgtacgcacaaatgtatggatatttgttgagccaaaaaaagaagtgaggtgctctg

- - - - - - - - - - - - - -  AGGATG