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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaattctaaagatttatagtttgctctgtaaaatccaggcatttcatggctgttttgtgtccttgcattgaatgatctgcacatgagtttatt...

Basic information

species Glycine max
transcript GLYMA02G01220.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01220.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os05g04340.2 (Oryza sativa), 5'ss of exon 9
CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaattctaaagatttatagtttgctctgtaaaatccaggcatttcatggctgttttg-tgtccttgcattgaatgatctgcacatgagtttatt
|||||||||||||| || ||||| || ||||||||||||||||| ||||||||||  || ||  |       |  |  |  |||  |           |  || |   |   |   | | ||  ||                          
CCTCTATTCCCTGGCGACAGTGGCGTTGATCAGCTTGTTGAAATCATCAAGgtaaattatatcttgcttccatcgaaatcactccctttttgttgtttacctcctacttaactgactattctctcag-------------------------

upper sequence: GLYMA02G01220.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os01g19150.4 (Oryza sativa), 5'ss of exon 8
CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaattctaaagatttatagt-ttgctctgtaaaatccaggcatttcatggctgttttgtgtccttgcattgaatgatctgcacatgagtttatt
||| | || |||||||| ||||| || || || |||||||||||||||||||||| ||    | ||      |  | | ||  ||| |  | |     | |||         |||  |  | ||||    |    ||| || | | |     
CCTGTTTTTCCTGGTGACAGTGGCGTCGACCAACTTGTTGAAATTATCAAGgtaacatctgatttagtttagtggaatattattctatgtagtttccccctttt-------cttttagctcatgcaggagacttactgtacttcattcag--

upper sequence: GLYMA02G01220.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G155836_T01 (Zea mays), 5'ss of exon 9
CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaattctaaagatttatagtttgctctgtaaaatccaggcatttcatggctgttttgtgtccttgcattgaatgatctgcacatgagtttatt
||||| |||||||| || || || || ||||||||||||||||| ||||||||||  ||             |||  ||  | |  | |||  |  |||| || | ||| ||   |    ||  ||   ||  ||| | ||          
CCTCTGTTCCCTGGAGAAAGCGGTGTTGATCAGCTTGTTGAAATCATCAAGgtaaacta------------ctatctttgtcccgattaaactcctgcatatcgttgct-ttacctccaatttaatctcatcctct-ctcag---------

upper sequence: GLYMA02G01220.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G075992_T01 (Zea mays), 5'ss of exon 5
CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaa-gataaattctaaagatttatagtttgctctgtaaaatccaggcatttcatggctgttttgtgtccttgcattgaatgatctgcacatgagtttatt
||| | || ||||| || ||||| || |||||||||||||||||||| |||||||   | | ||||    ||| |   |||    ||  |  | ||  ||||||   | ||  |  ||       |||      || |              
CCTGTTTTTCCTGGGGACAGTGGTGTCGATCAGCTTGTTGAAATTATTAAGgtaatagtgacttctttcaattgaagatttagcttgctagttaca--catttc-cagttgactcatggaggcttatttttctttcag--------------

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|193455275|gb|FK419252.1|FK419252
EST:     GGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: GGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|193403349|gb|FK367699.1|FK367699
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCGGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|207824407|gb|GD793767.1|GD793767
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAAACCCCGACAAGGGAAGAAATCAAGT
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAA-CCCCGACAAGGGAAGAAATCAAGT
EST: gi|193398127|gb|FK361249.1|FK361249
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCGGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|15286220|gb|BI470111.1|BI470111
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|10254836|gb|BE822602.1|BE822602
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|298195934|gb|HO044325.1|HO044325
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|7590534|gb|AW706284.1|AW706284
EST:     AGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: AGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|9259545|gb|BE347700.1|BE347700
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
EST: gi|37994511|gb|CF806247.1|CF806247
EST:     CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAG                         GTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC
genomic: CTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaa ... tcacatgcagGTTTTAGGAACCCCGACAAGGGAAGAAATCAAGTGTATGAATCCTAATTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCTATTCCCTGGTGAGAGTGGAGTAGATCAGCTTGTTGAAATTATCAAGgtaagataaattctaaagatttatagtttgctctgtaaaatccaggcatttcatggctgttttgtgtccttgcattgaatgatctgcacatgagtttatt

- - - - - - - - - AGTGGA
- - - - - - - - -  GTGGAG
- - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - -  TCAGCT