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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGTTAAGTGACCGGTTCCCACAACCATATCCAAATGAGCAAGCAGCCCGTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcag

Basic information

species Oryza sativa
transcript LOC_Os05g23620.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G032367_T01 (Zea mays), 5'ss of exon 4
TAAGTTAAGTGACCGGTTCCCACAACCATATCCAAATGAGCAAGCAGCCCGTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatattttatgccattggcgttgcattgtt-taatcttccaccttcaagttgtaatttactgtttg-actccgtatgttcag
|||  | || || || || ||||| || ||| ||||||||||||||||||| ||||| |||||||| || ||||| || || || ||||||||||| ||||||||   | || |||   ||| | |||| ||| | |   ||| |||       || |   |||||||||| | | | |   | |||
TAAACTCAGCGATCGCTTTCCACAGCCTTATGCAAATGAGCAAGCAGCCCGATTTGCTAATGGTGGCGCCTACCCGCCGGACCTTAGTCTTATCACAAAGgtaattgcagttaatggtgttg-cattgctttgatgtggcctttcact----gattatggcttactgtttgcattgcattcatccag

upper sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 4
TAAGTTAAGTGACCGGTTCCCACAACCATATCCAAATGAGCAAGCAGCCCGTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatattttatgccattggcgttgcattgtt-taatcttccaccttcaagttgtaatttactgtttg-actccgtatgttcag
|||  | || || || |||||||| || ||| |||| |||||||||||||| ||||| |||||||| |||||||| || || || ||||| ||||| |||||||| | |  | ||    || ||  ||   |||| | ||||||||         | |   ||||||||   | | |     |||||
TAAACTGAGCGATCGCTTCCCACAGCCTTATGCAAACGAGCAAGCAGCCCGGTTTGCTAATGGTGGTGCATACCCTCCGGACCTTAGTCTCATCACAAAGgtaattacagctaattt--tttgcagtgatctgttgtgatcttccattgcg----tatggcttactgttcacaatgcaatcattcag
















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|55408838|gb|CV721214.1|CV721214
EST:     CCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCG
genomic: CCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAAT-GGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCG
EST: gi|27547605|gb|CA765614.2|CA765614
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29655598|gb|CB651873.1|CB651873
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|58682709|gb|CK071396.1|CK071396
EST:     CAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: CAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|3768179|gb|AU032206.1|AU032206
EST:     AAATGGTGGGNNATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: AAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29659241|gb|CB655516.1|CB655516
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|86522378|gb|CI162584.1|CI162584
EST:     TTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTACTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: TTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGT-CTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|88844350|gb|CI005723.1|CI005723
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29670618|gb|CB666893.1|CB666893
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|5003486|gb|AU068635.1|AU068635
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
EST: gi|29674160|gb|CB670435.1|CB670435
EST:     GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAG                         GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT
genomic: GTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatat ... gtatgttcagGCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGTTAAGTGACCGGTTCCCACAACCATATCCAAATGAGCAAGCAGCCCGTTTTGCAAATGGTGGGGCATACCCACCAGATCTCAGTCTTATCACGAAGgtaatgatattttatgccattggcgttgcattgtttaatcttccaccttcaagttgtaatttactgtttgactccgtatgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG