Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattgtgtttggatggtgcatggcaaaagtagcaacttctttttcttaccaattttgaatgatttataacaattgtaaaatgcttaatttgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAATAACTACAACACAG

Basic information

species Glycine max
transcript GLYMA06G02580.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G02580.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 4
------aaattgtgtttggatggtgcatggcaaaagtagcaacttctttttcttaccaattttgaatgatttataacaattgtaaaatgcttaatttgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAATAACTACAACACAG
       | |    |||        | |  ||  |||||   |||    ||||  ||  |   |||  ||      || || ||| |  | |  ||  ||||||||||||||| || ||||||||||| ||| ||||||||||||||||||| || || |||||| | |||
acttatcactcaaatttaagcttgccttctcattagtagtc-cttaaccttctcccc--tcgcgaaatataccct-cagttttaataatcct--ttacatctgcagATCTTCGGGATGATAAGCAATTCTTTGTAGACCACCCTGGTGCAGTGCCTATTACTACAGCTCAG
















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|31561454|gb|CD487292.1|CD487292
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
EST: gi|4396727|gb|AI495724.1|AI495724
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCANNTTTTTATAGACCACCC
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCC
EST: gi|120533487|gb|EH261620.1|EH261620
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
EST: gi|4313831|gb|AI460950.1|AI460950
EST:     GGCATTATGCCCCCTGGTGTTCCAATAANTTCTCGTTGGACCAAAGTTAG                         ATCTTCGAGAAGATAAGCAA
genomic: GGCATTATGCCCC-TGGTGTTCCAATAA-TTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAA
EST: gi|298164350|gb|HO013995.1|HO013995
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
EST: gi|16348169|gb|BI973764.1|BI973764
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
EST: gi|10845271|gb|BF068427.1|BF068427
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTAT
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTAT
EST: gi|6483101|gb|AW202293.1|AW202293
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTNGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCCAATTTTTTATAGACCCACC-TGGTGCAGTACC
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGC-AATTTTTTATAGACC-ACCCTGGTGCAGTACC
EST: gi|19269284|gb|BM885540.1|BM885540
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
EST: gi|17021451|gb|BM092485.1|BM092485
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
EST: gi|19052868|gb|BM731535.1|BM731535
EST:     AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAG                         ATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA
genomic: AAGGCATTATGCCCCTGGTGTTCCAATAATTCTCGTTGGAACAAAGTTAGgtaagccttt ... tgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaccaattttgaatgatttataacaattgtaaaatgcttaatttgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAATAACTACAACACAG
      aattttgaatgattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattgtgtttggatggtgcatggcaaaagtagcaacttctttttcttaccaattttgaatgatttataacaattgtaaaatgcttaatttgatctgcagATCTTCGAGAAGATAAGCAATTTTTTATAGACCACCCTGGTGCAGTACCAATAACTACAACACAG

- - - - - tggatgg
- - - - - - - - - gcatggc
- - - - - - - - - - - - - - - - -caacttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgctt