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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttccaatctatttccacatttttctaactttcttccataaatgcttaatctatttatctatttatttttcctag

Basic information

species Glycine max
transcript GLYMA12G36520.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 5'ss of exon 16
GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttccaatctatttccacatttttcta--actttcttccataaatgcttaatctatttatctatttatttttcctag
|||||||| ||||| || |||||||| |||||||||||||||||||| || |||||||| |||||||||||||| || |||||||| |||||||| | | || || | ||| |||| ||| | | || || | | | ||| | | |
TCTTGAGAAGAGGGTCAATAAGAAAGTTATGGCAATGTTTGAGAAGGCAGAGGATGAGTATAATGATTTGATGTCAAAGAAAAACATCATTGAGgtgggtctta-ccttttctagtgataacctaggacttactttaaaagcagcatacgtaaaccttttgttttcatctgcag-

upper sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G006452_T02 (Zea mays), 5'ss of exon 10
GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttccaatctatttccacatttttctaactttcttccataaatgctta-atctatttatctat-ttatttttcctag--
|||||||| ||||| || |||||||| |||||||||||||||||||| || ||||||||||||||||||||||| || |||||||| || |||||| | ||| ||| || | || |||| | | || | | | | | |||| | || || | | ||
TCTTGAGAAGAGGGTCAATAAGAAAGTAATGGCAATGTTTGAGAAGGCGGAGGATGAGTACAATGATTTGATGTCAAAGAAAAACATCATCGAGgta-tctcctatc-atgtaca-gttttcttgataaactgaaagtagttttaatatctgggcacataccttgtctcatctgcag

upper sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 17
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 5'ss of exon 16
GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttccaa----tctatttc-cacatttttctaactttcttccataaatgcttaatctatttatctatttat--ttttcctag
|| |||||||| ||||||||||| || | ||| ||||||||||| ||||||||||| || |||| | | ||| |||| ||||| ||||| ||||| | || ||| | || | ||| || || || | | | | | | ||| | | ||| | ||||| |||
TCTAGAGAAAAGAGTGAACAAGAAGGTCACGGCTATGTTTGAGAAAGCTGAAGATGAATATAATGCTCTTATGACCAAGAAAAATATAATCGAGgttagttttggagggtctgtgcaacatagtttaaaaagcttaaaacacatttacgaactatgtttttttttttttcattttcttag

upper sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 17
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 5'ss of exon 16
GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttccaatcta---------tttccacatttttctaactttcttccataaatgcttaatctatttatctatttatttttcctag
| || ||||| ||||||||||| || ||||| ||||||||||| || |||||||| ||||||| | |||| || |||||||| | || ||||| | || || | ||| || | || || | | | ||| | || | | | ||||||||||
CTTGGAAAAAAGAGTGAACAAGAAGGTTATGGCTATGTTTGAGAAAGCAGAAGATGAATACAATGCTCTGATATCGAAAAAAAATACTATCGAGgttagttacagaggacagagggcctttgcaatgtatttcaatagcttcgtgtgccatcataacacaattttttcggtttttttcctag

upper sequence: GLYMA12G36520.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 5'ss of exon 16
GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgt----aatttccaatctatttccacatttttctaactttcttccataaatgcttaatctatttatctatttatttttcctag
|| |||||||||||||| |||||||| ||||||||||||||||| || ||||||||||||||||| || || ||||| |||| |||||||||||| | | |||||| || || || | || | || | ||| | | ||| | || |
CCTGGAGAAAAGGGTGAATAAGAAAGTTATGGCAATGTTTGAGAAAGCAGAAGATGAGTACAATGAATTAATATCCAAGAAAAGCATAATTGAGgtttgtagctctcaatctgttgacatgttgtcatactatgattttacttatgataa---tatgcctttaatag----------

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|58022904|gb|CX709645.1|CX709645
EST:     GCCTGAAGATGAGTACAATGATTTGATGTCCNNNNNNNNNCATAATTGAG                         AATGACAAGTCTAAAATCAAGATGGTGA-TGAAAGAGCTAGATGAGAAGAA
genomic: GGCTGAAGATGAGTACAATGATTTGATGTCC-AAAAAAAACATAATTGAGgtaatttcca ... tttttcctagAATGACAAGTCTAAAATCAAGATGGTGATTG-AAGAGCTAGATGAGAAGAA
EST: gi|58016495|gb|CX703237.1|CX703237
EST:     GGCTGAAGATGAGTACAATGATTTGATGTCCNNNNNNNNNCATAATTGAG                         AATGACAAGTCTAAAATCAAGATGGTGATTGAAGAGCTAGATGAGAAGAAG
genomic: GGCTGAAGATGAGTACAATGATTTGATGTCC-AAAAAAAACATAATTGAGgtaatttcca ... tttttcctagAATGACAAGTCTAAAATCAAGATGGTGATTGAAGAGCTAGATGAGAAGAAG
EST: gi|208208138|gb|GE003397.1|GE003397
EST:     AATGATTTGATGTCCAAAAAATACATAATTGAG                         AATGACAAGTCTAAAATCAAGAAGGTGATTGAAGAGCTAGATGAGAAGAAG
genomic: AATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttcca ... tttttcctagAATGACAAGTCTAAAATCAAGATGGTGATTGAAGAGCTAGATGAGAAGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAGgtaatttccaatctatttccacatttttctaactttcttccataaatgcttaatctatttatctatttatttttcctag

- - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - AAGATG