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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttactattactaaaacttctttcccaaatttgtcttctccatttcattcatttaatttctaatatacttttgctcttag

Basic information

species Glycine max
transcript GLYMA08G39880.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g50620.2 (Oryza sativa), 5'ss of exon 6
GATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttactattactaaaacttctttcccaaatttgtcttctccatttcattcatttaatttctaatatacttttgctcttag
| |||||||| | ||||||||| ||| |||| |||||||| |||||| | || || || |||||||||||||| ||  | || || || ||| | ||||||||| |  |||| |    | ||||     |  |||      || |      |  |||   |  ||||||  |  || |  |||
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCTCCAACAAAAAAGATGTGGAAGAgtatgt-ttatttc----atttctcattta--tttaaagattcaaccatcctgctttg--tattaatatcttgatgtttctag

upper sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os03g21914.1 (Oryza sativa), 5'ss of exon 6
GATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtat-ttactattactaaaacttctttcccaaatttgtcttctccatttcattcatttaatttctaatatacttttgctcttag
| |||||||| | ||||||||| ||| |||| |||||||| |||||| | || || || |||||||||||||| ||  | || || |||||| | ||||||||| ||  | | | |    |||  ||   | |||   |    |   ||  |  ||| |  |  | || |  | | |       
GTTGCATGGCTTCTCTTTCTGCCATGATTCAGCTTGAACTTCCTCATATCAACATTCTTTCAAAGATGGACCTGGTCGCCAACAAAAAGGATGTGGAAGAgtatgtttatttcatttctcctttatttaaagattcaaccatcctgctttgt--attaatctcttgatgttttctag-------

upper sequence: GLYMA08G39880.1 (Glycine max), 5'ss of exon 7
lower sequence: Vv00s0174g00200.t01 (Vitis vinifera), 5'ss of exon 6
GATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgta--tttactat------tactaaaacttctttcccaaatttgtctt-ctccatttcattcatttaatttctaa--------tatacttttgctcttag
| |||||||||| ||||||||| ||||| ||||| ||| | |||||||||||||| ||||| || ||||||||||| || || || | |||| |||||||||     |  |||       |||| | | |  |||   |  ||||  |  |  ||||  ||  | | || |  |         |||| ||||||||| ||
GTTGCATGGCATCTCTTTCTGCAATGGTCCAACTCGAATTGCCTCATGTTAATATTCTCTCCAAAATGGACCTTGTAACGAACAAAAGGGATATTGAAGAgtgggcctcttatgcacttcactatatcctacttcttgatgttgttctattttattttctttttctgatattcatgtcatttttatatttttgctctcag

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|37995842|gb|CF807431.1|CF807431
EST:     AATATCCTCTCAAAGATGGACCTTGTGACTANAAAGAAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
EST: gi|209724732|gb|BW651475.1|BW651475
EST:     TCTCAAAGATGGACCTTGTGACTAAAAATAAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: TCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
EST: gi|192306146|gb|FG996578.1|FG996578
EST:     AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
EST: gi|51341249|gb|CO982566.1|CO982566
EST:     AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
EST: gi|12690127|gb|BG156463.1|BG156463
EST:     AAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: AAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
EST: gi|192297924|gb|FG993203.1|FG993203
EST:     AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
EST: gi|9903086|gb|BE612054.1|BE612054
EST:     AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGA                         TTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT
genomic: AATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttacta ... ttgctcttagTTTTTTGGATCCAGAGCCCACCTTTTTATTGTCTGAATTGAATCAACGGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCATGGCATGTCTTTCTGCGATGGTTCAACTTGAACTACCTCATGTTAATATCCTCTCAAAGATGGACCTTGTGACTAAAAAGAAGGATCTTGAAGAgtatttactattactaaaacttctttcccaaatttgtcttctccatttcattcatttaatttctaatatacttttgctcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA