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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTCATTGCATCTCCCGAAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcattcctgcttataagataccagaataatgctatgaagaccgtccttggttgtcagcattcttatacacaatgataatctttgtttttcatgggtag

Basic information

species Oryza sativa
transcript LOC_Os01g08700.8
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.4 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G107101_T01 (Zea mays), 5'ss of exon 12
ATGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTCATTGCATCTCCCGAAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcattcctgcttataagataccagaataatgctatgaagaccgtcct-tggttgtcagcattcttata-cacaatgataatctttgtttttcatgggtag
 |||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| || || ||||| |||||||| | ||   | ||||||||   || || |   | ||||||| |     | | ||||| |||||||||||  |  |||||  ||| |||||| ||||| ||||
GTGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTCATAGCTTCTCCTGAAATGCAGATGTCTGCAGAAAGTACATCAGCTCACCAAGGATGGAGGAAGgtatgtttatgtgttcttataag---cccgagtggcggtatgaagtcatcaatattgttgttagcattcttatggctaaatgaccatccttgtttctcatgtgtag

upper sequence: LOC_Os01g08700.4 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM5G844173_T01 (Zea mays), 5'ss of exon 11
ATGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTCATTGCATCTCCCGAAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcattcctgcttataagataccagaataatgctatgaagaccgtccttggttgtcagcattcttata-cacaatgataatctttgtttttcatgggtag
 |||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||||||||| || || ||||| |||||||  | ||   | ||||||||    |                     |   | ||||| ||||||||| |  |  ||||| |||| |||||| ||| | ||||
GTGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTCATAGCTTCTCCCGAAATGCAGATGTCTGCAGAAAGCACATCAGCTCACCAAGGATGGAGGAAGgtataattatgtgttcttataagccttc---------------------tttattgttgttagcattcttgtggctaaatgacaatccttgtttctcacgtgtag
















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|29668032|gb|CB664307.1|CB664307
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|29680917|gb|CB677192.1|CB677192
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|86848173|gb|CI290653.1|CI290653
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|58689941|gb|CK078628.1|CK078628
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|38477853|gb|CF961986.1|CF961986
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|58611835|gb|CK039547.1|CK039547
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGAC
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGAC
EST: gi|33675400|gb|CF303639.1|CF303639
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTNTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA
EST: gi|8335705|gb|BE040522.1|BE040522
EST:     AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAG                         GTTGTGGATGCGCTTTGTGACGTTGTTTCAGCCTCACCGACCAAGGCTTCA
genomic: AAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcat ... tcatgggtagGTTGTGGATGCGCTTTGTGACATTGTTTCAGCCTCACCGACCAAGGCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCTTCTCTGTTGTCTCATTGCTCTGGCAGAAGCTCATTGCATCTCCCGAAATGCAGATGTCTGCAGAAAGTACATCAGCTCATCAGGGTTGGAGAAAGgtatggtcattcctgcttataagataccagaataatgctatgaagaccgtccttggttgtcagcattcttatacacaatgataatctttgtttttcatgggtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA