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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagcattattggaattcctttgctattgccactgacattcaactatctaattacctctatacaatcttgtactttgtgtaatgaag

Basic information

species Oryza sativa
transcript LOC_Os01g42490.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42490.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G034430_T01 (Zea mays), 5'ss of exon 13
GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagcat--tattggaattcctttgctattgccactga--cattcaactatctaattacctctatacaatcttgtactttgtgtaatgaag
||||||||||| |||||||| |||| |||||| || || || ||||| |||||||||||||| ||||||||||| |||||||||||||||| ||  ||  || || |  |  |    | |   |||  |  |||||||| |||||||    |    |   | ||  | |||           
GATTTTGAAGGAACAAAAGACGCCAGCAAGGAACCACTGGTGACAAGCTACAACAGAAAATTCATGGGAACAGTAGACTACATATGgtaaacaactatcctactgaagataatgcaatgtaaacacccaagcattcaacgatctaatg---tggcaatcgtgttacaatttag---------
















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|157650229|gb|EX449863.1|EX449863
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|86480117|gb|CI122750.1|CI122750
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|87027334|gb|CI270009.1|CI270009
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|29624406|gb|CB629417.1|CB629417
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|86858239|gb|CI271125.1|CI271125
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|2800930|gb|AA754224.1|AA754224
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTKTWCAAGTGCTAGATACCTTCCCAAAA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAA
EST: gi|29624470|gb|CB629481.1|CB629481
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|87013807|gb|CI271198.1|CI271198
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|58690956|gb|CK079643.1|CK079643
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|29624531|gb|CB629542.1|CB629542
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|58677956|gb|CK066643.1|CK066643
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|86480856|gb|CI123489.1|CI123489
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|29635013|gb|CB640022.1|CB640022
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|88901588|gb|CI001696.1|CI001696
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
EST: gi|29637193|gb|CB642202.1|CB642202
EST:     CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATG                         GGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA
genomic: CTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagc ... tgtaatgaagGGCTTCCGAAGATCTGCAGACTGTTCAAGTGCTAGATACCTTCCCAAAAGA

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTTTGAAGGGACAAAAGATGCCAACAAGGAGCCTCTAGTAACAAGTTACAACAGAAAATTTATGGGAACAGTGGACTACATATGgtaaataagcattattggaattcctttgctattgccactgacattcaactatctaattacctctatacaatcttgtactttgtgtaatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA