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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatttgaactttgaactttctttgaactgcacatcctcatgtttgcgctctctttccttccagttgtaagctacacagtaccttactttcattttgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAAACTTGGTTGAAATTGATCCTTTAGCATCTCTTCCAAAGCTGCACTTCCT

Basic information

species Glycine max
transcript GLYMA20G18440.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G18440.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0150g00590.t01 (Vitis vinifera), 3'ss of exon 3
gtacaatttgaactttgaactttctttga-actgcacatcctcatgtttgcgctctctttccttccagttgtaagctacacagtaccttactttcattttgtatt-gcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAAACTTGGTTGAAATTGATCCTTTAGCATCTCTTCCAAAGCTGCACTTCCT
    ||  |||   |   | |   |||   | |    ||    || || | |      |    | | |||  |          || |||   |     ||  ||| ||||||| ||||||||| |||||||| |||||||| || |||||| |  |||| |||||||  || ||||||||  |  ||||  ||||||||||||| |||||
--gtaagctgagaatgatattgggtttatcattatttattaatattttggggtcacaatgttcttctgttacacaagcttagatatcttttatggtgcttaaatttgcagAGTACTTGCCAAAATTACACACGCTAGTTCTTACGAACAACCGGCTTGTCAACTTGGCAGAGATTGATCCCCTTTCATCCTTTCCAAAGCTGCAGTTCCT
















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|192294286|gb|FG986375.1|FG986375
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
EST: gi|192326367|gb|FK017669.1|FK017669
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
EST: gi|19054300|gb|BM732967.1|BM732967
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
EST: gi|7588075|gb|AW703878.1|AW703878
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
EST: gi|192305354|gb|FG994036.1|FG994036
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
EST: gi|23728179|gb|BU762135.1|BU762135
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
EST: gi|298192581|gb|HO033015.1|HO033015
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAG
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAG
EST: gi|151394202|gb|EV264073.1|EV264073
EST:     AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAG                         AGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA
genomic: AATGCTCATTAACAACAACAGGATTACTAGAATTAATCCCAACATCGGAGgtacaatttg ... tgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctttccttccagttgtaagctacacagtaccttactttcattttgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAAACTTGGTTGAAATTGATCCTTTAGCATCTCTTCCAAAGCTGCACTTCCT
                              accttac  putative branch site (score: 3)
                               ccttactttcatttt  CT-rich tract
                                     tttcattttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaatttgaactttgaactttctttgaactgcacatcctcatgtttgcgctctctttccttccagttgtaagctacacagtaccttactttcattttgtattgcagAGTTCTTGCCAAATTTACACACTCTAGTTCTCACAAACAACAGAATTGTAAACTTGGTTGAAATTGATCCTTTAGCATCTCTTCCAAAGCTGCACTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC