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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaacaaaactacttattgagatgattaaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcag

Basic information

species Glycine max
transcript GLYMA04G39490.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G046098_T02 (Zea mays), 5'ss of exon 2
GCTTGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgta----------atgaacaaaact--acttattgagatgattaaattttatcatcattgttggtgtgct-tattcatttagttttgaatctgcag
|| |||||   |||||| || ||||||||||| |  ||||||||||||||||||||          |  |||  | ||  || | |||  ||   || || | | | |   |||  |  || | ||||  ||  |||||   |||||||
GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgcccttcacaataactgagctaaacatgttgccatagctatatat-accttttatgtatgcatgatatatttcttgtgttttatgtctgcag

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G046098_T04 (Zea mays), 5'ss of exon 2
GCTTGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgta----------atgaacaaaact--acttattgagatgattaaattttatcatcattgttggtgtgct-tattcatttagttttgaatctgcag-----
|| |||||   |||||| || ||||||||||| |  ||||||||||||||||||||          |  |||  | ||  || | |||  ||   || || | | | |   |||  |  || | ||||  ||  |||||   |||||||     
GCATGCTGTGCTGTTCTTCAAAGTTGGGTCTCAAGAAAATTTATGACTGGATGgtacgcccttcacaataactgagctaaacatgttgccatagctatatat-accttttatgtatgcatgatatatttcttgtgttttatgtctgcagtgtag

upper sequence: GLYMA04G39490.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 5'ss of exon 2
GCTTGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaacaaaactacttattgagatgat-taaat-ttta-----tcatcattgttggtgtgctta---ttcatttagttttgaatctgcag
|||||||| | | |||||||||| |||||||| ||||| || ||||||||||||||||   |  | |||    || | ||  | || || ||||     |  | ||| ||     || ||   || | ||  |||||||  |||||
GCTTGCTGTTATTTTCTCCAGAGCTGGGTCTCAAAGAAGTTCATGACTGGATGgtaatatgcttacctatgccttaatatattctagatgtttactcattttttattattttccagcctaacattgagttgattttgaaattgcag

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|254330499|gb|GR841764.1|GR841764
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|9901349|gb|BE610317.1|BE610317
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|9564106|gb|BE473615.1|BE473615
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|22523553|gb|BU082355.1|BU082355
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|151407101|gb|EV276916.1|EV276916
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|8284138|gb|BE021697.1|BE021697
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|151397141|gb|EV267014.1|EV267014
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|151405159|gb|EV274973.1|EV274973
EST:     TGCTGCTTTATTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
EST: gi|31561519|gb|CD487357.1|CD487357
EST:     TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTTTGACTGGATG                         CGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT
genomic: TGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaaca ... gaatctgcagCGTAGTTCTTTTTCCAGTTGCTGTTACCTTCTTCATTACATGGTGGTTTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGCTGCTTTGTTCTCCAGAGTTGGGTCTCTAAGAAATTTATGACTGGATGgtaatgaacaaaactacttattgagatgattaaattttatcatcattgttggtgtgcttattcatttagttttgaatctgcag

-  TGCTGC
- - GCTGCT
- - - - - - - - - - - - - - - -  AAGAAA