Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccagtttctagaatgttgaagattatcttaaaaataaagttttatggttgacctgacagatcgtgaccaatcaactatgctttgtaatgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC

Basic information

species Glycine max
transcript GLYMA08G39880.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39880.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 3'ss of exon 4
ttgccagtttctagaatgttgaagattatcttaaaaataaagttttatggttgacctgac---agatcgtgaccaatcaactatgctttgtaatgttt-tgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC
 || |  |  |  |  | |  | |   ||  | | | ||   |    || || || | ||   | ||| |||| ||| |   |  |    || ||||| | |||| ||||| ||||| |   | ||||||||||| ||    || ||||| ||||||||||||||||||||||| |  ||||||||||| ||| | ||||||||
atgtccttcccctgtctttgcatgggaattctgaga-tattttagattgtttaacttcacctaaaatcatgac-aatgag--agaccacatattgtttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGGAAAAATTTCAACGTTTGTGCTGTGTACCTTCTTGATTC

upper sequence: GLYMA08G39880.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 3'ss of exon 4
ttgccagtttctagaatgttgaagattatcttaaaaataaagttttatggttgacctgac---agatcgtgac--caatcaactatgctttgtaatgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC
 || |  |  |  | | |||| |    |  |   |||||   |    || || || | ||   | ||| ||||    |   || |    ||||    || | |||| ||||| ||||| |   | ||||||||||| ||    || ||||| |||||||||||||| |||||||| |  |||||||| || ||||| ||||||||
atgtccttcccctgta-gttgcatgggaattctgaaatattttagattgtttaacttcacctaaaatcatgacaatgagagaccacatcttgt----ttctccagGCCAGATTGAACTCTTCACTCATGTCCCAGTTCTGCGTAACTTTGTTGAACATTTGAAACGAAAAAATTTCAACGTTTGTGCCGTGTACTTTCTTGATTC

upper sequence: GLYMA08G39880.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 3'ss of exon 4
ttgccagtttctagaatgttgaagattatcttaaaaataa---agttttatggttgacctgacagatcgtgaccaatcaactatgctttgtaatgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC
 ||||  |  | |  |  |        |   |  | ||       |||| |  |   |  ||  |||| | |  |||    |   |||   | |  |||  ||| |||||||| || | ||| ||||| ||| |||||  |||||||||||| |||||||| || || ||||| | |||||||||||| ||| | ||||||||
-tgcccttgcccaatagatatgcacccagtatgcatattgtttgttttttttttcagctggattgatc-ttataaattctttggtcttcaca-ttctttatagGCCAGATAGAGCTTTTTTCGCATGTTCCAATGCTTCGGAATTTTGTGGACCATTTGAAGCGTAAGAATTTCAATGTTTGTGCTGTGTACCTGCTTGATTC

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|17021922|gb|BM092956.1|BM092956
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGTCCCAGTGCTTAA
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAA
EST: gi|192306146|gb|FG996578.1|FG996578
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGCCCCAGTGCTTAAGAATTTTGTGGAAC
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
EST: gi|51341249|gb|CO982566.1|CO982566
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
EST: gi|192299207|gb|FG988665.1|FG988665
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
EST: gi|209724731|gb|BW651474.1|BW651474
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAG
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAG
EST: gi|209716787|gb|BW665465.1|BW665465
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATT
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATT
EST: gi|192297924|gb|FG993203.1|FG993203
EST:     TTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
genomic: TTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
EST: gi|192306145|gb|FG996577.1|FG996577
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGCCCCAGTGCTTAAGAATTTTGTGGAAC
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
EST: gi|192297923|gb|FG993202.1|FG993202
EST:     GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTG                         GTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC
genomic: GGAACTGGACAATTATTTAGATGATGATTACTTGGTTTTCGACTGCCCTGgtattcatgc ... tgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatggttgacctgacagatcgtgaccaatcaactatgctttgtaatgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC
        acctgac  putative branch site (score: 3)
                                          taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccagtttctagaatgttgaagattatcttaaaaataaagttttatggttgacctgacagatcgtgaccaatcaactatgctttgtaatgttttgcagGTCAGATAGAACTATATTCACATGTCCCAGTGCTTAAGAATTTTGTGGAACATTTGAAACGGAAAAATTTTAGTGTTTGTGCTGTTTACTTACTTGATTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT