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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGACTGAAGCTTTGGCACAAGCAGGTCTTGAATCATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagaccacttcttgttttgaattctgtttctttatatttgctttgtgctgtgctggtagcctattacttgcgaattagtagtgttattatataca...

Basic information

species Oryza sativa
transcript LOC_Os06g40650.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G345544_T02 (Zea mays), 5'ss of exon 3
GTGACTGAAGCTTTGGCACAAGCAGGTCTTGAATCATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac--cacttcttgttttg------------aattctgtttctttatatttgctttgtgctgtgctggtagcctattacttgcgaa-ttagtagtgttattatataca
||||||||||||||||| |||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||  ||||    | ||| | ||||             | || ||||||| ||| | | || |||||||  |||||| |  |||||   | ||  ||  ||              
GTGACTGAAGCTTTGGCGCAAGCAGGCCTTGAATCTTCAAATCTTATCGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttcgcagatgatatttccttttttactttagatacatacttgtgtttctctatgtatactctgtgctgcactggta-ctcattacacactaagctaccag--------------

upper sequence: LOC_Os06g40650.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G071659_T01 (Zea mays), 5'ss of exon 3
GTGACTGAAGCTTTGGCACAAGCAGGTCTTGAATCATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagaccacttcttgttttgaattctgtttctttatatttgc-tttgtgctgtgctggtagcctattacttgc-gaattagtagtgttattatataca---
|||||||||||||||||||| ||||| |||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||  || | |   | |   ||    ||| ||| ||      |||||||   ||    | ||| |   ||| | | | |||     |||| | ||    
GTGACTGAAGCTTTGGCACAGGCAGGCCTTGAATCTTCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttagcagatgacatttccctcttt-tttcacttcattagatgcatacttgtgcttctctat--gtctactctgtgctgcactggtac--acattacacactaag
















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|116875525|gb|EC366033.1|EC366033
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAGAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|116875559|gb|EC366067.1|EC366067
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|33677878|gb|CF306117.1|CF306117
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|58692386|gb|CK081073.1|CK081073
EST:     ATC-AATCTTATTGTAGGC-TTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|58671660|gb|CK060346.1|CK060346
EST:     AAATCTTCATTGTAGGCAGTTGATTTTACAAGAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCGCGATGTCTGCATGATATTGGAAACACTCCA
genomic: AAATCTT-ATTGTAGGCA-TTGATTTTACAA-AGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGC-CGATGTCTGCATGATATTGGAAACACTCCA
EST: gi|29632713|gb|CB637722.1|CB637722
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|300216150|gb|HO087935.1|HO087935
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|58695004|gb|CK083691.1|CK083691
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
EST: gi|33677349|gb|CF305588.1|CF305588
EST:     ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAG                         GTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA
genomic: ATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagac ... tctccattagGTAAACTTTCCTTCAATCGCCGATGTCTGCATGATATTGGAAACACTCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGACTGAAGCTTTGGCACAAGCAGGTCTTGAATCATCAAATCTTATTGTAGGCATTGATTTTACAAAGAGCAATGAATGGACAGgttaacagaccacttcttgttttgaattctgtttctttatatttgctttgtgctgtgctggtagcctattacttgcgaattagtagtgttattatataca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA