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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAATAAATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgtaattgaggttctgttgctg...

Basic information

species Glycine max
transcript GLYMA03G42370.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G42370.3 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os02g54340.1 (Oryza sativa), 5'ss of exon 1
--ATCAAATAA--ATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgtaattgaggttctgttgctg-
    |    |   |||||  | || |  ||||||||  ||| | | |||||||| |||||||| ||||||||||| |||||||| || ||||| ||||| ||  || ||| |||  |   ||  |  |  |  |    || |  |  |    |   || | |   |   |  |     |             |  |||  | |  
GCGGCGGGGAGCCATGGCGCCGGAGCCGGAAGACGACATCATGAACGAGAAGAACCCCCGCCCGCTCGACGAGGACGACATCGCTCTCCTCAAGACCTACgtgagtgtccccccgctagatc--tccctgatctc---ttcccatctaggggtgctttctggtgatctggtcccatggtgggctcgggcctcgggctggggttag

upper sequence: GLYMA03G42370.3 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os06g09290.2 (Oryza sativa), 5'ss of exon 1
----ATCAAATAAATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgta---attgaggttctgttgctg
         |   |||||  | || |  || |||||  ||| | | |||||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| ||  ||  ||  |   ||    |  | ||    | |   ||||  ||           |||      | | |||||  |  ||  |    ||  ||| |        
GGAGGGGGGAGCCATGGCGCCGGAGCCCGAGGACGACATCATGAACGAGAAGAACCCGCGCCCGCTCGACGAGGACGACATCGCCCTCCTCAAGACCTACgtgagtgccccgcagatcggatcgatccccctctcgt-cttctcctcctagggtggaaattcttcggccgatctgagcttgattcacgggttagggtcccc------

upper sequence: GLYMA03G42370.3 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G110185_T01 (Zea mays), 5'ss of exon 1
----ATCAAATAAATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgtaattgaggttctgttgctg
    |  | |   |||||  | || |  || || ||| | | | | ||||||||||||||||| |||||||||||||||||||| || ||||||||||||||  ||  |        | ||    |  |   ||| | | || |    | |   |  | ||||   |  | |||         |   |||  | | ||||    
CAGGAGGACAGCCATGGCGCCGGAGCCGGAGGATGATATTATGAACGAGAAGAATCCCCGCCCGCTCGACGAGGATGACATCGCGCTCCTCAAAACCTATgtgcgtgacacgatccccgtttggatctctc-ttatgatctcgtggatctagggttgt-ttggtgctttggtctcgggggcgggcctttggagctgtgttcg--

upper sequence: GLYMA03G42370.3 (Glycine max), 5'ss of exon 1
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 1
----ATCAAATAAATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaatta---tatgtaattgaggttctgttgctg--
    |  | |   |||||  | || |  || || ||| | | | | ||||||||||||||||| ||||||||||| |||||||| || ||||||||||||||  ||  |    |  || ||    |  |         | |  | ||     ||||   ||   |      | || |||    || |   | |  ||| |||| |    
CAGGAGGACAGCCATGGCGCCGGAGCCGGAGGATGATATTATGAACGAGAAGAATCCCCGCCCGCTCGACGAGGACGACATCGCGCTCCTCAAAACCTATgtgcgtgcctcgaccctcgtttggatctc---------tctgatctcgtggatctagggttctttggtgattttgtattggggtagggcttaggagttgtgttccctcg

upper sequence: GLYMA03G42370.3 (Glycine max), 5'ss of exon 1
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 5'ss of exon 1
ATCAAATAAATGGCAAC----TGAACAT-GAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgtaattgaggttctgt-tgctg
  | |       ||| |     | |||| |  |||||| |     | |||||||| || | ||| ||||| |||||||||||||| || ||||||||||||||  ||   ||   |||  |       | |  |  | ||    |    ||  | |   || ||  ||  ||   ||||| | | |   || | || ||| | |||
-CCGAGCTCCGCGCAGCATGGCGGACATCGCCGACGATCTTCTCAAGGAGAAGAACCCGCCCCCGCTCGATGAGGATGACATCGCACTGCTCAAAACCTATgtgagtgcgct---tttggtcttgacgcgagctccgtgtcgtgtgatgccgtttt-cgatcggtcttgggcgtggaatt-tgtatctctgcgtttttgtcttctg

upper sequence: GLYMA03G42370.3 (Glycine max), 5'ss of exon 1
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 1
----ATCAAATAAATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcc-tccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgtaattgaggttctgttgctg-
             |      | ||   ||  |||||| |     | |||||||| ||   ||| ||||||||||| ||||||||||||||||||||||||||| ||  || |  | ||| ||   |  |    || | ||   ||  | | | | |   |   || |  ||  |   |||   ||       | |   |    || 
TCCAGCTCTGCGCACCATGGCGGACATTGCCGACGATCTACTCAAGGAGAAGAACCCGGCCCCGCTCGACGAGGACGACATCGCCCTTCTCAAAACCTATgtaagtgcccatgtccttccttt--tcgcagtttttgcgtcatttgccgcaaatttgg-acccgcctcgagaac---atttagtgcggcctcgatgtagaatgtgt

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|151405667|gb|EV275481.1|EV275481
EST:     TCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACC----TAT                         GGTTTGGGGCCTTATTCCACCAGCATNNNNNNNGCCGAGAAGGAGATCAAA
genomic: TCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccc ... tgcaatgcagGGTTTGGGGCCTTATTCCACCAGCATAAAAAAAGCCGAGAAGGAAATCAAA
EST: gi|213589227|gb|DB957759.1|DB957759
EST:     TCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACC----TAT                         GGTTTGGGGCCTTATTCCACCAGCATNNNNNNNGCCGAGAAGGAAATCAAA
genomic: TCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccc ... tgcaatgcagGGTTTGGGGCCTTATTCCACCAGCATAAAAAAAGCCGAGAAGGAAATCAAA
EST: gi|213602675|gb|DB956611.1|DB956611
EST:     TCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACC----TAT                         GGTTTGGGGCCTTATTCCACCAGCATNNNNNNNGCCGAGAAGGAAATCAAA
genomic: TCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccc ... tgcaatgcagGGTTTGGGGCCTTATTCCACCAGCATAAAAAAAGCCGAGAAGGAAATCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAATAAATGGCAACTGAACATGAAGACGATTTCAAGGATGAGAAGAATCCCCGCCCCCTCGACGAGGATGACATCGCCCTTCTCAAAACCTATGTATgtatcctccctttcattccattaccaaattagggtttcttttcaccactctattattggctttcagctctgaattatatgtaattgaggttctgttgctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctt