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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCAACTCTTGCTTTATCCAAATGCTTCAGATCCTCTCAATGGTGATGCAGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatatttgtatgttgggctactttttctgatcatttaagacaagtattataatggtttcctattgtagtctatgatccaaccgcagtgcctatga...

Basic information

species Glycine max
transcript GLYMA05G01980.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G01980.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv17s0000g07960.t01 (Vitis vinifera), 5'ss of exon 7
CCCCAACTCTTGCTTTATCCAAATGCTTCAGATCCTCTCAATGGTGATGCAGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatattt-gtatgttgggctac---tttttctgatcatttaagacaagtattataatggtttcctattgtagtctatgatccaaccgcagtgcctatga
|| || |||||||||||||||||||||||||| || || |||||||||||||||||  | ||||||||| | ||||| |  |||||  | ||||| |||||| |   | |||   |  |     ||    |   |||       ||  |||| |   || |    |||  |  | |   |   ||   |  | |  | ||||  
CCACAGCTCTTGCTTTATCCAAATGCTTCAGACCCACTTAATGGTGATGCAGCATCAATGATGATGAAGAACAAAGATCAATATGAGAAAAAAGTAAAAGgtaaaagtttttcacacatataaatatggatgcatctaggagagtataacaacttgaattagaacttc--accgaaactttccatttgattggaa-gtctatc-
















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|298181365|gb|HO022804.1|HO022804
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAA
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAA
EST: gi|13788151|gb|BG650743.1|BG650743
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         ATTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
EST: gi|298184467|gb|HO029680.1|HO029680
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAAG
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAG
EST: gi|10232163|gb|BE801051.1|BE801051
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACTGCTG
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
EST: gi|12687894|gb|BG154290.1|BG154290
EST:     GCATCGTTAATGATGAAAGATTAAGAGCTGTTTGACCAGAAAGGTTAA-G                         AGTATTGGGAGCCGTATGCT
genomic: GCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAG-TTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCT
EST: gi|58025024|gb|CX711765.1|CX711765
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
EST: gi|151411773|gb|EV281584.1|EV281584
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAGAAGGAAAACATTTGCAACTCTACGGCTG
EST: gi|298185117|gb|HO030330.1|HO030330
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAAG
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAG
EST: gi|18721187|gb|BM523328.1|BM523328
EST:     AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAG                         AGTATTGTGAGCGGTATGCTAAGAAGGAAAACATT
genomic: AGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatat ... gtggggacagAGTATTGTGAGCGGTATGCTAAGAAGGAAAACATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCAACTCTTGCTTTATCCAAATGCTTCAGATCCTCTCAATGGTGATGCAGCATCGTTAATGATGAAGGATAAAGAGCTGTATGACCAGAAAGTTAAAGgtgagcatatttgtatgttgggctactttttctgatcatttaagacaagtattataatggtttcctattgtagtctatgatccaaccgcagtgcctatga

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