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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggcaaaacaattcaattatatagttttcagtatcattttctgcatattgtttgtttctgatggtttaacatattgtttgattaacag

Basic information

species Glycine max
transcript GLYMA04G02530.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G02530.3 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 2
GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggcaaaa--caattcaattatatagttttcagtatcattttctgcatattgtttgtttctgatggtttaacatattgtttgattaacag
|| |||||||| || |||||||||||||||||||| |||||||| || ||||| ||||| || ||  |||| ||||||||||| ||||||||  |    ||   |  |     | | | | ||    ||||| ||||  ||  ||  |||||| | ||   | |  |||||   |  | |||||
GATTATGTGCCAACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTGgtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctca--tttcttgtttttaat---tgactatattcgattttgaacag

upper sequence: GLYMA04G02530.3 (Glycine max), 5'ss of exon 2
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 5'ss of exon 2
GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggcaaaacaattcaattatatagttttcagtatcattttct-gcatattgtttgtttctgatggt-ttaacatattgt-ttgattaacag---
|| || || || ||||| |||||||| ||||| || ||||| ||||| |||||||  ||||| ||||| || || ||||||||||| ||| | |    |    |   |||     |   | ||  |   || | || |  |     | |     | |||| || |    | ||  |    ||  |   
GATTACGTTCCTACCGTGTTTGACAACTTCAGCGCAAATGTAGTGGTCGATGGAAATACCGTCAACCTCGGGTTATGGGATACAGCAGgtgagagatgatttgacgccaagctcttctctatcgttcatatctactcgagttccaatcgacagcgctggtattgatgcgtagtgcttccgaatggaaa

upper sequence: GLYMA04G02530.3 (Glycine max), 5'ss of exon 2
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 5'ss of exon 3
GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggcaaaacaattcaattatatagttttcagtat-cattttctgcatattgtttg--tttctgatggtttaacatattgtttgattaacag-------
|| || || || ||||| |||||||||||||| || ||||| ||||| ||||||| ||| || || || ||||| ||||||||||| |||||    |  | |  |||| | || |   | | |  | | | | || ||  || |||  |  |  | | || |    || |||  || |  |   |       
GATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAGgtaa----gagacaggattcgactagaatctctcctttgtacctattgtggttactgtcgggatcacgggtgctgattcacattaatttaggacgggcgctgca

upper sequence: GLYMA04G02530.3 (Glycine max), 5'ss of exon 2
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 5'ss of exon 2
GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggcaaaacaattcaat---tatatagttttcagtatc--attttctgcatattgtttgtttctgatggtttaacatattgtttgattaacag------
|| || || || ||||||||||| || ||||| || ||||| || || ||||||| ||| |||||||| ||| | ||||||||||| ||||| | |  ||   || |   |     | | |  ||  | | |  |||    || | |||| ||      | ||     |  | ||   ||  || |       
GATTACGTTCCTACCGTTTTTGATAACTTCAGCGCGAATGTCGTTGTCGATGGAAACACTGTAAACCTTGGACTATGGGATACAGCAGgtaaga-gataacttaagttggtgttcttttggcatttcgcagctgattactagcgttttgtatggc----aagggcatccgcagtgaccgaccaataattcaat

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|58014216|gb|CX700958.1|CX700958
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|14258618|gb|BG881526.1|BG881526
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAAGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|207827775|gb|GD800368.1|GD800368
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|9563948|gb|BE473457.1|BE473457
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|192331824|gb|FK024928.1|FK024928
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|207836636|gb|GD806633.1|GD806633
EST:     GTGGTTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: GTGG-TGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|58021086|gb|CX707828.1|CX707828
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
EST: gi|151393592|gb|EV263467.1|EV263467
EST:     TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG                         GTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG
genomic: TGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggc ... tgattaacagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTGgtaacatggcaaaacaattcaattatatagttttcagtatcattttctgcatattgtttgtttctgatggtttaacatattgtttgattaacag

- - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG