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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTAGGAGACATGGAGATATAATCAAAAGAACTGTTGGAGGCCATTTTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatcatccactatatttatgtttatagctccatccatctcccagttctactcttttttttaatcagctaaaaaatgattgatatatatatatat...

Basic information

species Glycine max
transcript GLYMA08G11980.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G11980.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv06s0004g00750.t01 (Vitis vinifera), 5'ss of exon 13
GTTCTTAGGAGACATGGAGATATAATCAAAAGAACTGTTGGAGGCCATTTTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatcatccactata-tttatgtttatagctc-catccatctcccagttctactcttttttttaatcagctaaaaaatgattgatatatatatatat
   || ||||||||||| || || || || || ||||| |||||| ||||||||||||||||  | ||||||||||| |||||| |||| || || |||||| | |||  | | |  |  ||| | | | | |        |||     |  | |||    ||  | ||| ||| ||  |       ||||      |  |
CACCTCAGGAGACATGGGGACATCATTAAGAGGACTGTAGGAGGCTATTTTGTTGTACAAGGCAGAGCTGATGACACCATGAATCTTGGGGGCATCAAGgtaccacattcttctcagtcctttctctcttttgtaagtgctcatgatgtaagt-tacaagcttactcaat-agccaatgagcctgccatatgccacaaggt
















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|207822576|gb|GD795659.1|GD795659
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|208341381|gb|GE139035.1|GE139035
EST:     CGGGCTGANGACATAATGAATATTGTTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: CGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|207778584|gb|GD750603.1|GD750603
EST:     CGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: CGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193695946|gb|FK640564.1|FK640564
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|208073722|gb|GD872819.1|GD872819
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|208303163|gb|GE101432.1|GE101432
EST:     GGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193337426|gb|FK303800.1|FK303800
EST:     TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193680472|gb|FK624378.1|FK624378
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193394127|gb|FK357712.1|FK357712
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|207711864|gb|GD693678.1|GD693678
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|208192749|gb|GD989786.1|GD989786
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|6848074|gb|AW350364.1|AW350364
EST:     TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193657917|gb|FK601944.1|FK601944
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|58018254|gb|CX704996.1|CX704996
EST:     TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|208104513|gb|GD904518.1|GD904518
EST:     GGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTATCTGTGATAGGGCCGACGAAGGCATT
genomic: GGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193393426|gb|FK358830.1|FK358830
EST:     CGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: CGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|207811266|gb|GD783397.1|GD783397
EST:     GAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193402267|gb|FK368480.1|FK368480
EST:     GGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|15815389|gb|BI787664.1|BI787664
EST:     TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193461963|gb|FK429416.1|FK429416
EST:     GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
genomic: GGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATTGAGCGTGTCTGTGATAGGGCCGACGAAGGCATT
EST: gi|193419911|gb|FK381979.1|FK381979
EST:     TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAG                         ACAAGTTCTGTAGAAATTAGAGCGTGTCTGTGATAGGGCCGACGAAGGCAT
genomic: TTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatc ... tgatatgcagACAAGTTCTGTAGAAATT-GAGCGTGTCTGTGATAGGGCCGACGAAGGCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTAGGAGACATGGAGATATAATCAAAAGAACTGTTGGAGGCCATTTTGTTGTACAAGGGCGGGCTGATGACACAATGAATATTGGTGGAATAAAGgtatcgcatcatccactatatttatgtttatagctccatccatctcccagttctactcttttttttaatcagctaaaaaatgattgatatatatatatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatctcc