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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttgcagggtatattttatcatggtagcgatgcttttagctacatttcattgatattttcatgtcatctcatggtttttgtggtgtgaaaatcttgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCTAGCGCTTATGCACGTCTCTATGATTATGAACGTGTACGCAAG

Basic information

species Glycine max
transcript GLYMA08G37270.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 7
gtattgttgcagggtatattttatcatggtagcgatgcttttagctacatttcattgatattttcatgtcatctcatggtttttgtggtgtgaaaatcttgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCTAGCGCTTATGCACGTCTCTATGATTATGAACGTGTACGCAAG
    | |   |     |  |  ||   | ||  ||||  | |  |||   ||| || ||   |   ||| |  |    | || ||||   | | |      || | ||| |||| |||  ||| ||||||||||| |||||| |||| |||||||| ||||| |||||||| |||||||||||||||| || | | ||||||
----tctgcgattaagttgtccatttagataa-gatgtgtctgtcta---ttcgtttatgcatatttgttag-tagaagcttgtgtgacttaatagctactaattgcagTTGGAAAAAAGTGCCACACTCTTCAGACCAAAACTAATAGTTGCTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACATATTCGCAAG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 7
gtattgttgcagggtatattttatcatggtagcgatgcttttagctacatttcattgatattttcatgtcatctcatggtttttgtggtgtgaaaatcttgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCTAGCGCTTATGCACGTCTCTATGATTATGAACGTGTACGCAAG
    | |   |  |  |  |  ||   | ||  ||||  | |  |||   ||| || ||   |   ||| |  |    | || ||||   | | ||     || | ||| |||| |||  ||| ||||||||||| |||||| |||| |||||||| ||||| |||||||| |||||||||||||||| |||| | ||||||
----tctgcgattgagttgtccatttagataa-gatgtgtctgtcta---ttcgtttatgcatatttgttag-tagaagcttgtgtgacttaataactactaattgcagTTGGAAAAAAGTGCCACACTCTTCAGACCAAAACTAATAGTTGCTGGTGCTAGTGCTTATGCCCGTCTCTATGATTATGCACGTATTCGCAAG

upper sequence: GLYMA08G37270.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 7
gtattgttgcagggtatattttatcatggtagcgatgcttttagctacatttcattgatattttcatgtcatctcatggtttttgtggtgtgaaaatcttgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCTAGCGCTTATGCACGTCTCTATGATTATGAACGTGTACGCAAG
    | |   |     |  |  ||   | ||  ||||  | |  |||   ||| || ||   |   ||| |  |    | || ||||   | | |      || | ||| |||| |||  ||| ||||||||||| |||||| |||| |||||||| ||||| |||||||| |                             
----tctgcgattaagttgtccatttagataa-gatgtgtctgtcta---ttcgtttatgcatatttgttag-tagaagcttgtgtgacttaatagctactaattgcagTTGGAAAAAAGTGCCACACTCTTCAGACCAAAACTAATAGTTGCTGGTGCTAGTGCTTATGCCC-----------------------------

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|151402224|gb|EV272037.1|EV272037
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCT
EST: gi|209699627|gb|BW655719.1|BW655719
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|6134799|gb|AW133192.1|AW133192
EST:     CGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|209699197|gb|BW656186.1|BW656186
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|120529377|gb|EH257511.1|EH257511
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTACTTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|213588396|gb|DB967882.1|DB967882
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|9439993|gb|BE440504.1|BE440504
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|120530707|gb|EH258840.1|EH258840
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|209724195|gb|BW659729.1|BW659729
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|209715019|gb|BW650870.1|BW650870
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|14205774|gb|BG839452.1|BG839452
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|17518985|gb|BM188027.1|BM188027
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|209700117|gb|BW652975.1|BW652975
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|209715940|gb|BW650957.1|BW650957
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|209727383|gb|BW651931.1|BW651931
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|120533233|gb|EH261366.1|EH261366
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
EST: gi|22539787|gb|BU089630.1|BU089630
EST:     CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAG                         ATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT
genomic: CAATGCCATATCGATTGAATGAAAGTACAGGATACATCGACTATGACCAGgtattgttgc ... tgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatattttcatgtcatctcatggtttttgtggtgtgaaaatcttgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCTAGCGCTTATGCACGTCTCTATGATTATGAACGTGTACGCAAG
 cattgat  putative branch site (score: 4)
                                      aaaatcttgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgttgcagggtatattttatcatggtagcgatgcttttagctacatttcattgatattttcatgtcatctcatggtttttgtggtgtgaaaatcttgaaatacagATGGAGAAATCTGCTACACTCTTCAGGCCAAAATTAATTGTTGCTGGAGCTAGCGCTTATGCACGTCTCTATGATTATGAACGTGTACGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT