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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtattgtagcgtggcatttcttgttagttccatattttctgacacatggaaggtgctgacctctctgtgtgtttgggtggcttgtgaag

Basic information

species Oryza sativa
transcript LOC_Os10g37730.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37730.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AC194389.3_FGT001 (Zea mays), 5'ss of exon 3
ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt--gtagcgtggcatttcttgttagttccatatttt--ctgacacatggaaggtgctgacctctctgtgtgtttgggtggcttgtgaag
|||||| ||||||| || || |||||||| |||||||||||||| ||||||||||| || || |||||||||||| |       |||   | | |  | || |  | | ||| ||||   |   ||| || | ||||| ||   | | ||| ||| ||  | ||  |   
ACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAATgtaagacggcacgtaagatagtacctttt-tctgctacattttttagttaggacaaggtaagtgctaactgttgtttgttttttggctgattcag---
















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|13420680|gb|AU174770.1|AU174770
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29682101|gb|CB678376.1|CB678376
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|88385475|gb|CI564135.1|CI564135
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29645490|gb|CB650497.1|CB650497
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29673129|gb|CB669404.1|CB669404
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29632141|gb|CB637150.1|CB637150
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGNNNNNNNCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29641797|gb|CB646804.1|CB646804
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29628246|gb|CB633257.1|CB633257
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29673087|gb|CB669362.1|CB669362
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29644924|gb|CB649931.1|CB649931
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
EST: gi|29615014|gb|CB620027.1|CB620027
EST:     GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT                         GTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA
genomic: GGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtatt ... gcttgtgaagGTTACCAGGGCGGATTACTTGAGTGGCCGAACAGCATTGCATTTCGCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAATgtatggtattgtagcgtggcatttcttgttagttccatattttctgacacatggaaggtgctgacctctctgtgtgtttgggtggcttgtgaag

- - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG