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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcttaaacctgctatcatttggaacatggttattaaacctgctatctttaacatcatactgtgtatttctaattaaacaaatcttttttgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC

Basic information

species Glycine max
transcript GLYMA18G47920.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47920.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0023g00820.t01 (Vitis vinifera), 3'ss of exon 7
aatcttaaacctgctatcatttggaacatggttattaaacctgct-atctttaacatc-atactgtgtatttcta-attaaacaaatcttttttgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC
  |  ||  | |    |  ||    |  | | || | | | || | |||||| | ||    | | | | || ||  |||| |  |   ||| ||  ||  ||||||||||| ||||| ||||||||   || || |||  ||||||||| ||||| | |||| ||||| | ||||||||||||||||||||||| 
--taatactcatttattgcttcatcatttagctaatcaccatgttcatcttttatatttgcattttatgttgcttcattatatcataatttgtt--ttacacagAGCTCCAGTATTTTCTGAAGAGATCCTCGGTGGGGAGGAGGGAGAGGGTGAAGGTGTAAAGCCAGTGGAAAGGTCCTTTTGGGCTAAATAT
















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|193618431|gb|FK572555.1|FK572555
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTCGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|254345763|gb|GR859410.1|GR859410
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207751867|gb|GD724084.1|GD724084
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACTAA                         GTGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|193325160|gb|FK291410.1|FK291410
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207753550|gb|GD725976.1|GD725976
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|193333542|gb|FK299488.1|FK299488
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208309007|gb|GE101679.1|GE101679
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTA
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTA
EST: gi|208085854|gb|GD882444.1|GD882444
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGG
EST: gi|254331915|gb|GR843658.1|GR843658
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208290698|gb|GE082790.1|GE082790
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208145882|gb|GD941407.1|GD941407
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGCGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208246680|gb|GE046224.1|GE046224
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTAAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGG
EST: gi|207734721|gb|GD710152.1|GD710152
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208134798|gb|GD927467.1|GD927467
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGG
EST: gi|193356816|gb|FK319564.1|FK319564
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGG-CTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208124293|gb|GD920505.1|GD920505
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207700941|gb|GD682830.1|GD682830
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTA
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTA
EST: gi|193380905|gb|FK348792.1|FK348792
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCGGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|254345762|gb|GR859409.1|GR859409
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|193340217|gb|FK307838.1|FK307838
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|193442901|gb|FK404251.1|FK404251
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCGGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207702293|gb|GD683048.1|GD683048
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207782115|gb|GD753686.1|GD753686
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207740907|gb|GD715853.1|GD715853
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAA-GCAGTGAACAGGCACCAA                         GAGACTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGT
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAG-CTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGT
EST: gi|208035516|gb|GD837680.1|GD837680
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGG
EST: gi|208256364|gb|GE051747.1|GE051747
EST:     AACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: AACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|208218438|gb|GE017506.1|GE017506
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
EST: gi|207790915|gb|GD760484.1|GD760484
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTT
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTT
EST: gi|192299870|gb|FG987828.1|FG987828
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAG-CACTTGGCGGGCTGGA
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGA
EST: gi|207727158|gb|GD704328.1|GD704328
EST:     GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAA                         GAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG
genomic: GTGGTCTTTCAAGTCACACACAGTTCTAAAAAGCAGTGAACAGGCACCAAggtatatgtt ... tgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttaacatcatactgtgtatttctaattaaacaaatcttttttgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC
                       ttctaat  putative branch site (score: 2)
                                      tcttttttgcttc  putative PPT
                  tgtatttctaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcttaaacctgctatcatttggaacatggttattaaacctgctatctttaacatcatactgtgtatttctaattaaacaaatcttttttgcttcaacaGAGCTCCAATATTTACTGAAGAGGCACTTGGCGGGCTGGAGGGAGACGGTGAGGCTGTACAGCCAATAGAAAGGTCCTTTTGGGCTAAATAC

- - - -aacctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa