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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatacatccacacagtatatgcctcaatgtttattcatttgtatattggaactttaaagtggaatataatgagtttgctcaacttcctcgaactattttgcttgttgtcttaacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

Basic information

species Glycine max
transcript GLYMA08G20020.1
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 31
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 11
-----------------------gttatacatccacacagtatatgcctcaatgttta--ttcatttgtatattggaactttaaa-gtggaatataatgagtttgctcaacttcctcgaac-tatt--ttgcttgttgtcttaacaaa-----------cagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
                       |||    ||  |   || | ||   |  |||| |   || | |||  ||||  |     | |  |   || |  |   ||   |  | |     |||  ||||   ||| |||||||| | |||            |||||| | || || || ||||| || |||||||| ||||| | ||| ||  |||| || |||||||| ||||||||||| || |||||||| ||||||||||
gtacgtgagctgcctttgcttgagttgagtatttaatgagaagatat-tagatgtctgcctttagttgagtatttcatgagaagatattagatgtcttcctttgagttgagtaatgagaagatattagatgcctgttgtctaaccaataatccaatggccagGATGTCATACCCCATATGGCCCAGGAATATGGATTTGAGTACGAGCTTGTCACATATAAATGGCCAACATGGTTGCACAAACAGAAAGAGAAGCAGCGAA

upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 31
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 31
--------gttatacatccaca-cagtatatgcctcaatgtttattcatttgtatattggaactttaaagtggaatataatgagtttgctcaacttcctcgaactattttgcttgttgtcttaa-caaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
         || |   |   |  |   ||||||||   ||| | |  || | ||||| |     |||       || | |     |     | |  | |  |  || | ||  |    |  ||| |   |||||| ||||||| || ||||| ||||||||    ||||| |  || || || || |||||||||||  | ||||||||||| |||||||||||||| ||||
gttggctccttgtttctttgcttccacatatgccttt-tgtgtttgtatctatatat-gtcttcttatctctagatgtgaacttatcttgtagccacattaacttaatgtgtatcgcattctaatcttgcagGATGTGATTCCACATATGGCACAAGAATACAACTTTGAGTATGAGCTGATTACATACAAATGGCCGTCCTGGTTGCATAAACAGAAAGAAAAGCAACGAA

upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 31
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 32
gttatacatccacacagtatatgcctcaatgtttattcatttgtatattggaactttaaagtggaatataatgagtttgctcaacttcctcgaactattttgc-ttgttgtcttaacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
    | || |||     | | |  |||    |||| |  ||||  | | |    |||    |  | || |   |||    |     |     |||| | ||   |||||  |||   |  |||||| | ||||| || ||||| || |||||||||||||| |  ||  | || || ||||||||||| ||||||||||||||||||||||||||||||||||
--gttgcaaccattt--tctttcactcttcttttagtgttttgactgtcgttgttttcttctaaattaaatgtagtcaatttcttatggggaaactctcttttgttgttaactttcaatgcagGATGTAATTCCACATATGGCACAGGAATATGGTTTTGAGTATGAGTTGATTACTTACAAATGGCCAACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

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|33389227|gb|CA852434.1|CA852434
EST:     GTCCAGTTAAATTCTGGTTCATAAAGAACTACCTGTCTCCTCCTTTTAAG                         GATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATC
genomic: GTCCAGTTAAATTCTGGTTCATAAAGAACTACCTGTCTCCTCCTTTTAAGgttatacatc ... taacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATC
EST: gi|15202166|gb|BI425257.1|BI425257
EST:     GTCCAGTTAAATTCTGGTTCATAAAGAACTACCTGTCTCCTCCTTTTAAG                         GATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATC
genomic: GTCCAGTTAAATTCTGGTTCATAAAGAACTACCTGTCTCCTCCTTTTAAGgttatacatc ... taacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatgagtttgctcaacttcctcgaactattttgcttgttgtcttaacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA
                                          tcttaac  putative branch site (score: 2)
                                       ttgtctt  CT-rich tract
                         aactatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatacatccacacagtatatgcctcaatgtttattcatttgtatattggaactttaaagtggaatataatgagtttgctcaacttcctcgaactattttgcttgttgtcttaacaaacagGATCTGATTCCTCACATGGCTCAAGAATATGGTTTTGAATGCGAACTAATCACCTACAAATGGCCTACATGGTTGCATAAGCAGAAAGAAAAGCAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA