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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGCGCTCCGCCGCTCGCTCGTCTTCTTCCGCGGCCAGCCCCTCGGCACCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagctattcgcggcggcggcgctttcggattgtgcggattcagctcatctggaaaccgcatggcttgtctcatctggggagcttttgctttgctttgctttgctcgcag

Basic information

species Oryza sativa
transcript LOC_Os02g34560.2
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g34560.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G118737_T01 (Zea mays), 5'ss of exon 1
GGAGGCGCTCCGCCGCTCGCTCGTCTTCTTCCGCGGCCAGCCCCTCGGCACCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggtta--gctattcgcggcggcggcgctttcggattgtgcggattcagctcatctggaaaccgcatggcttgtctcatctggggagcttttgctt---tgctttgctttgctcgcag----------------
|||||||||||||||||| |||||||| ||||||||||||||||| |||||| | |||||| |||||||||| |||||||| ||||||||||||||||| || || |    || |        ||  |   | | ||   |    | |    |  |    |           || | |       |    | |   |     ||||   | |  ||   |                
GGAGGCGCTCCGCCGCTCCCTCGTCTTGTTCCGCGGCCAGCCCCTTGGCACCGTTGCCGCCGTCGACCACGCGTCCGAGGAAGTCCTCAACTACGACCAAgtgggctgccactctattttatagctccctctactgaaaattaataattgttttgttgacagcagttgaaaattattttgatcccgagcttgtcattcggacgcttaaatatcttctggggtaaccggctgggcag

upper sequence: LOC_Os02g34560.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G170842_T01 (Zea mays), 5'ss of exon 1
GGAGGCGCTCCGCCGCTCGCTCGTCTTCTTCCGCGGCCAGCCCCTCGGCACCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagctattcgcggcggcggcgctttcggattgtgcggattcagct--catctggaaaccgcatggcttgtctcatctggggagcttttgctttgctttgctttgctcgcag
|||||||||||||||||| ||||||||||| |||||||||||||| |||||| | |||||| |||||||||| |||||||| ||||||||||||||||| || || | |  | ||         || |  ||   |||||   | |    |   |  || ||    |||   |  | ||   | |  |    | |  |   | |   ||        
GGAGGCGCTCCGCCGCTCCCTCGTCTTCTTTCGCGGCCAGCCCCTTGGCACCGTTGCCGCCGTCGACCACGCGTCCGAGGAAGTCCTCAACTACGACCAAgtgggct-gtcactccattttatagctccctc---ttgtgaaaaattgattattacttgtaatagacat---tcatatcgcttagaaaa---tggtataaatgtatattc-------
















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|58662491|gb|CK051177.1|CK051177
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
EST: gi|58609058|gb|CK037091.1|CK037091
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTC
EST: gi|29632226|gb|CB637235.1|CB637235
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
EST: gi|58665870|gb|CK054556.1|CK054556
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
EST: gi|58656839|gb|CK045519.1|CK045519
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTACGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
EST: gi|29677237|gb|CB673512.1|CB673512
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
EST: gi|58696107|gb|CK084794.1|CK084794
EST:     CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAG                         GTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC
genomic: CCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagc ... ttgctcgcagGTGTTCGTGAGGGATTTCGTGCCGAGCGCGCTGGCGTTCCTGATGAACGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGCGCTCCGCCGCTCGCTCGTCTTCTTCCGCGGCCAGCCCCTCGGCACCATCGCCGCCTTCGACCACGCCTCCGAGGAGGTCCTCAACTACGACCAGgttggttagctattcgcggcggcggcgctttcggattgtgcggattcagctcatctggaaaccgcatggcttgtctcatctggggagcttttgctttgctttgctttgctcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG