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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgattgatagttgattgtatactatagttgttattttttttcctgtttgaagaaattttattttccgttcatacttatgtagaccttttcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG

Basic information

species Glycine max
transcript GLYMA10G01550.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G01550.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g19510.1 (Oryza sativa), 3'ss of exon 6
agtgattgatagttgattg-tatactatagttgtt-attttttttcctgtttgaagaaattttattttccgttcatactta---tgtagaccttttcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
      |  |  | || || | |  | ||| | |  || ||   |   |||  |   | ||   || | |  ||||  | |   | | |      |  |  |||||||||||||||||||||| || || ||||||||||
-----gtacttttggaatgctctcttttagctatccatcttgccttaagttgcattgatttcggttatgcactcattttcactgttttgtttccctttttggcagTATGGGAGCTTTTCTGCTTAGTGCTGGGACAAAAG
















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|7795792|gb|AW781189.1|AW781189
EST:     AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAG                         TATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
genomic: AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAGgtaacctttt ... tcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
EST: gi|11689956|gb|BF597632.1|BF597632
EST:     AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAG                         TATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
genomic: AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAGgtaacctttt ... tcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
EST: gi|31561455|gb|CD487293.1|CD487293
EST:     AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAG                         TATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
genomic: AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAGgtaacctttt ... tcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
EST: gi|16279786|gb|BI943616.1|BI943616
EST:     AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAG                         TATGGGAGCCTTTCTGCTGAGCGCAAGGACCAAAAG
genomic: AGGCATATCCGACCTGATGTGTCTACTGTTTGTGTTGGATTAGCAGCTAGgtaacctttt ... tcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGAC-AAAAG
EST: gi|209714325|gb|BW665587.1|BW665587
EST:     TTTGTGTTGGATTAGCAGCTAG                         TATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
genomic: TTTGTGTTGGATTAGCAGCTAGgtaacctttt ... tcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgaagaaattttattttccgttcatacttatgtagaccttttcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG
                                        ccttttcatct  CT-rich tract
      aagaaattttatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgattgatagttgattgtatactatagttgttattttttttcctgtttgaagaaattttattttccgttcatacttatgtagaccttttcatctgcagTATGGGAGCTTTTCTGCTGAGCGCAGGGACAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
-gtgattg
- - - - - - - - - - - - - - - - - - - - - -cctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtag