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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaaaatattgtagcatgatatcagcaattttattttaagttgtttgccatggagtagttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG

Basic information

species Glycine max
transcript GLYMA07G05170.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 3
---aggaaaatattgtagcatgatatcagcaattttattttaagttgtttgccatggagtagttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
      ||  ||  |||   | ||    || | |   | |||      |    ||  |   || |  | ||||   ||| || |||   | ||| | |  |||||||||||||||| || ||||| ||||| ||||||||||
tgctacaagttagggtatttttatcctcgctacta-gtgttactgcactatttatataaatgtagtcaattgagtttgaact-attgggttttattcta-cagATTATGTGTTGGAAGGCAGTGAGGGAACGCCTTTTGCAG

upper sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 3
aggaaaatattgtagcatgatatcagcaattttattttaagttgtttgccatggagtagttgatacttgat---actgaccttattctat---gttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
         ||  ||  |  |   |  | |  |   || |||   ||   | ||     |||||   | |    | |    |||  ||||    ||||| |  ||||||||||| |||| || ||||| ||||||||||||||||
----gggagtttcagtct--ttctattattactgcatttagtatgttaaaaagggtagcttgatctcttactaaaatagagttaaactattggattaatcttacagATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAG

upper sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 4
aggaaaatattgtagcatgatatcagcaattttattttaagttgtt--tgccatggagtagttgatac-ttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
 | |  || || |    | |  |     |||||||| |    | ||  |    | ||| | |||  || |||||  |    || | |||  || |||| |||||||||||| ||||||||||||| |||||||| |||||||
ggtattatgtttttctctcactttcctgattttattatggtctattaattttcttgagcatttgtaaccttgatttta---ttctcctaccttgatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG

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|193518256|gb|FK476597.1|FK476597
EST:     GATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: GATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|213589359|gb|DB961692.1|DB961692
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|120495095|gb|EH223262.1|EH223262
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|24205463|gb|BU964716.1|BU964716
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|207707971|gb|GD692496.1|GD692496
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|9902562|gb|BE611593.1|BE611593
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|7692130|gb|AW760244.1|AW760244
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|298173240|gb|HO020224.1|HO020224
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|298163944|gb|HO013589.1|HO013589
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|120491908|gb|EH220075.1|EH220075
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|193440118|gb|FK408519.1|FK408519
EST:     TGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: TGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|9264559|gb|BE352706.1|BE352706
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCTCCAAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgccatggagtagttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
                                 ttattctatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaaaatattgtagcatgatatcagcaattttattttaagttgtttgccatggagtagttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA