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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagctctataggatagggtaacatctaattgggtttatacttaattgatctttggttttgtcttttgcttaagttcatacttatcatcaaggcaacctaaccttcaagtttttgcttgtag

Basic information

species Glycine max
transcript GLYMA15G11350.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G11350.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 5'ss of exon 4
GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagctctataggata---gggtaacatctaattgggtttatacttaattgatctttggttttgtcttttgcttaagttcatact-tatcatcaaggcaacctaaccttcaagtttttgcttgtag
||||| || |||||||| || |||||||||||||| ||||||||| ||||| | || || || |||||||| ||  | || |||||  |||   |   |    |      ||| || | |  ||  |  ||   ||||  |   ||| || |    ||   |||| ||| ||     || |||                                
GTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGTTTGTTCACCTTTACTGCTGCTTATTTACCTTGGgtaagtatttttagtttcctttccatgtacca-caacatgactacatgactaatgcacacttgattctcatcttaagttaacttcctagagcctcttcata------------------------------

upper sequence: GLYMA15G11350.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G04860.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgta-agctctataggatagggtaacatctaattgggtttatacttaattgatcttt--ggttttgtcttttgcttaagttcatacttatcatcaaggcaacctaaccttcaagtttttgcttgtag
|| || || ||||||||||||||||| |  ||||||||||| ||||| ||||| || || ||||| || || ||||| ||||||||| ||  | |||| | |  |     ||| || |   |  |  |||  |||    |  |     || || |||||||                                                     
GTCTATGTATGGAGCAAACAAAATCCTTATATTCACATGAGTTTCCTTGGTCTGTTCACCTTCACAGCAGCTTACCTACCATGGgtgagtttaactctctcgtttccctaaacttccaccggaatgaataaataacatcttctgcaaattctggcttttgcag---------------------------------------------------
















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|151394524|gb|EV264395.1|EV264395
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|58023286|gb|CX710027.1|CX710027
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|15287660|gb|BI471551.1|BI471551
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|58016888|gb|CX703630.1|CX703630
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|151397563|gb|EV267436.1|EV267436
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|9203644|gb|BE329868.1|BE329868
EST:     ACATGAGCTTTCTGTGTCTCTTTACTTGCACTGCTGCCTACCTTCCATGG                         GTTCTACTTGGG-TTCTCTGTACTC
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCT-CTTGGGGTTCTCTGTACTC
EST: gi|151400841|gb|EV270655.1|EV270655
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|23731152|gb|BU763683.1|BU763683
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|213608886|gb|DB980784.1|DB980784
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|120532687|gb|EH260820.1|EH260820
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|10236465|gb|BE805353.1|BE805353
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA
EST: gi|214006459|gb|DB987212.1|DB987212
EST:     ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGG                         GTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTT-GG-GCATCTA
genomic: ACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagc ... ttgcttgtagGTTCTCTTGGGGTTCTCTGTACTCGTTGGTGCTAGTGCTTGGGTGGATCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTACGTGTGGAGCAAACAAAATCCCTTCATTCACATGAGCTTCCTGGGTCTCTTTACTTTCACTGCTGCCTACCTTCCATGGgtgcgtaagctctataggatagggtaacatctaattgggtttatacttaattgatctttggttttgtcttttgcttaagttcatacttatcatcaaggcaacctaaccttcaagtttttgcttgtag

- - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC