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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaattataaatttttggagcatctatccctttgaaatttctttacttcattcatctgtctttttactatgttgctgacatagtttataatatcctgaacag

Basic information

species Glycine max
transcript GLYMA09G34310.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 3
GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaattataaatttttggagcatctatccctttgaaatttctttacttcattcatctgtctttttactatgttgctg---acatagtttataat-atcctgaacag
||| ||||||||||||| || || ||||| || || || ||||| ||||| ||||||||||| || ||||| ||||| || || || |||| |  |       |  ||   |   || |    || | |    | |  || ||   |  |  | | |||  |    | ||||| ||  |  |  ||     
GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTATAACTTTGGAGAACTGCTTGCTCATCCAATTgtaag-aattctgtacc----aaaaattcctgatttcgtgccttttctttcacctgtatttgaactgatgttgttttgaagtatgcttagttgattgtcgttgtg-----

upper sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ34882 (Selaginella moellendorffii), 5'ss of exon 3
GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatta-taaatttttggagcatctatccctt-tgaaatttctttacttcattcatctgtctttttactatgttgctgacatagtttataatatcctgaacag
|| ||||| || || |||||| |  | || || || || |||||||| |||||||||||||| || ||||| ||||||||||| || |  |  |   | |||   |  | | | |||  || | |        ||  ||| ||| |||                                         
GACCTGGCTTTCGACTTGTCCTTGGCAGCGCTCCTAGGAGATAACATTTACAACTTTGGAGAACTTCTTGCGCATCCTATAgtaagcagctggtgtttctttctcgtcttttttcctcgtgtactgagaggtttttgttcttctatctcag--------------------------------------
















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|11413942|gb|BF426017.1|BF426017
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAAAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|151394684|gb|EV264555.1|EV264555
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGAC
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGAC
EST: gi|19269301|gb|BM885557.1|BM885557
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|17518751|gb|BM187793.1|BM187793
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|151403199|gb|EV273009.1|EV273009
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAG-TGGAATGGCTTTACTATATTCTGCAC
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|151412996|gb|EV282804.1|EV282804
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|254334177|gb|GR849095.1|GR849095
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|23726775|gb|BU761390.1|BU761390
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|192328077|gb|FK020380.1|FK020380
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGAC
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGAC
EST: gi|298190509|gb|HO032630.1|HO032630
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTCGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|120493180|gb|EH221347.1|EH221347
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAAGAGCCTTCTGG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAA-GAGCCTTCTGG
EST: gi|19053931|gb|BM732598.1|BM732598
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|8402724|gb|BE058358.1|BE058358
EST:     TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAN
genomic: TTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
EST: gi|208143212|gb|GD942846.1|GD942846
EST:     CTACTTGCCCATCCTATA                         ATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG
genomic: CTACTTGCCCATCCTATAgtgagtaatt ... tcctgaacagATTAAGAGCCTTCTGGGGACAAAGGTGGAATGGCTTTACTATATTCTGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCTGGCATTTGATTTGTCCCTCTCTGCCCTTCTTGGGGATAACATCTACAACTTTGGAGAGCTACTTGCCCATCCTATAgtgagtaattataaatttttggagcatctatccctttgaaatttctttacttcattcatctgtctttttactatgttgctgacatagtttataatatcctgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT