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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgcttccttagttgctttacttgtcttgccaccctctcctcttaagaacttcattaacttaactttcattttag

Basic information

species Glycine max
transcript GLYMA02G46380.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 3
--------CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgcttccttagttgctttacttgtcttgccaccctctcctcttaagaacttcattaacttaactttcattttag
        | | || || |||||||| ||||||||||| |||||||| |||||||||   || ||  ||||||||||||||||     |   |  |    ||  ||       ||   ||| |  ||  | |  || |||     || |||| |     | |                          
ATGACTGTCCGTGAAGCGCTGAACTCTGCACTCGATGAAGAAATGTCTGCTGATCCTTCTGTTTTTCTGATGGGTGAAGAGgt-----acacttggaactcactcact-----ttctctccctgatttgtgtgtttttctaag-gccttctctttcgtggcag-------------------------

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os08g42410.2 (Oryza sativa), 5'ss of exon 2
CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgcttcc-ttagt----tgctttacttgtcttgccaccctctcct------cttaagaacttcattaacttaactttcattttag---------------
  | || ||  |||| || || || |||||||| ||||| ||||| |||   || ||||||||||| ||||||||||| ||||| || || ||||| |||||  ||   ||   ||||     |||| |  ||| |     | | |  | |       ||  |||    |   | | ||  |||  |||                 
GCGTGAAGCATTGAATTCTGCCCTTGATGAGGAGATGTCTGCTGACCCTTCTGTTTTCTTGATGGGAGAAGAGGTTGGAGAATACCAAGGGGCATATAAGgtgagtaatttttattagaccaatgctgtctttggcccattatcatgacataattaatttctgaatactaaatagtaaagcttctctttcctgcaacattttgcag

upper sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 4
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 4
--------CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgcttccttagttgctttacttgtcttgccaccctctcctcttaagaacttcattaacttaactttcattttag
        ||| || ||||| || || ||| | |||||||||||||| |||||||||||||| ||  | ||||||||||||||| |    |  |||    |||    | |   ||  |     | || ||   |   | |    | |   || | |     |  |  |||   ||             
ATGACAGTCAGAGATGCTCTAAATTCTGCAATTGATGAGGAAATGTCTGCTGATCCTAAAGTATTTGTCATGGGTGAAGAGgttag----ttgcagctaacatgtttgataaattcatcttgcaatttctaatcagatatcaatatctcatctttt-----atcttgttattgtag------------

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|8826851|gb|BE210581.1|BE210581
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCANGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|4292147|gb|AI441863.1|AI441863
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|192295237|gb|FG986956.1|FG986956
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|298167466|gb|HO012729.1|HO012729
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|208287126|gb|GE082228.1|GE082228
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|208157640|gb|GD954103.1|GD954103
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|213594578|gb|DB957997.1|DB957997
EST:     AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: AAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
EST: gi|207780409|gb|GD752218.1|GD752218
EST:     TTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAG                         ATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT
genomic: TTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgct ... ttcattttagATATCCAAGGGGCTGCTCGACAAGTATGGCCCCGAGAGGGTTCTCGATACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGAGGCTCTGAACTCCGCACTCGATGAGGAAATGTCAGCTGATCCTAAAGTGTTCTTGATGGGTGAAGAGGTTGGGGAATATCAGGGTGCATACAAGgttggttgcttccttagttgctttacttgtcttgccaccctctcctcttaagaacttcattaacttaactttcattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG