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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttcccggttatctttcatccttcttgtgttttgtcattgttttgatgttttcaacttatgggacag

Basic information

species Glycine max
transcript GLYMA12G03660.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03660.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv03s0038g02380.t01 (Vitis vinifera), 5'ss of exon 3
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaag--tatagtttcccggttatctttcatccttcttgtgttttgtcattgttttgatgttttcaacttatgggacag---------------------------------------------------------------------------------------------------------------------
|| || ||||||||||| ||||||||||||||||||||||| || |||||||| |||||||| ||||| ||||||||||||||||| |||||   |  ||       |  ||  ||  | |   || |  ||||   |  |||   || | |||   ||    | |                                                                                                                      
GATTATGTGCCAACTGTATTTGACAATTTCAGTGCAAATGTTGTGGTGGATGGGAGCACTGTTAATCTAGGGTTGTGGGATACTGCAGgtaaagttccagacctgtaggaattgtttgttcacatttt--tttgaggtactttgcttgctctcagggtaaaaaatacattgttcttaaaggcaaacaaaaactactttaaagatgctgtctcaatggttgtcttaccactacacctctttgagggttcttaatattgaactgattttgttaatttatggaacag

upper sequence: GLYMA12G03660.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 5'ss of exon 3
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttcccggttatctttcatccttcttgtgttttgtcattgttttgatgttttcaacttatgggacag-----------------------
|| ||||| ||||| || |||||||||||||| |||||||| || || ||||||| ||| || ||||| || || |||||||| || ||||||          ||  ||   |   |||||  |   | ||||  ||  | |   | |  |   |  ||   ||                        
GATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAGgtaagagacaggattcgactagaatctctcctttgtacctattgtggttactgtcgggatcacgggtgctgattcacattaatttaggacgggcgctgca

upper sequence: GLYMA12G03660.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 2
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttcccggttatctttcatccttcttgtgttttgtcattgttttgatgttttcaacttatgggacag
||||||||||| || |||||||| || || ||||| ||||| || |||||||| | |||||||||| | ||  | ||||| || ||||||| || ||| |             |  | ||            |  ||| |||  |||||       ||    |||
GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttagctggaaaaactcggcttgttctaacgcaaacgcatgcttgctttt-tgtttctcgtaaatctcgcag

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|58014286|gb|CX701028.1|CX701028
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|58020948|gb|CX707690.1|CX707690
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|151401174|gb|EV270988.1|EV270988
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGCTTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|308222701|gb|HO760611.1|HO760611
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|58021197|gb|CX707939.1|CX707939
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298170161|gb|HO018785.1|HO018785
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|192329144|gb|FK021131.1|FK021131
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
EST: gi|298172850|gb|HO019834.1|HO019834
EST:     TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTG                         GCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG
genomic: TGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatag ... tatgggacagGCCAAGAAGATTACAATAGATTAAGACCCTTAAGCTATCGTGGAGCAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttcccggttatctttcatccttcttgtgttttgtcattgttttgatgttttcaacttatgggacag

- - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG