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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA

Basic information

species Glycine max
transcript GLYMA06G36620.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 3
-ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatt-tgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA
  ||    | || |||  |  | || |  | |||| || |  | ||||| || |        | |  ||||| | ||| ||| |  |  ||  |  |||||| | || |||||||||||||| ||||||||||| || ||||| ||  |||||||| | || || || || || ||||| ||  | || || |||||||| |
cctaaaattcatagtggattctattgtatatttgtatgctagaataattgtggtaagaaaatccttatttgactagatactgatgctgatctta--ttgcagGTGACCCACATGGAAATGATCAAAGGAATCAAAGGTCATGGCTACCATGATGAATTGGTCATTCCTATTATTGAGAATACCCCTTATGAGTATGAGCTCA

upper sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G53850.3 (Arabidopsis thaliana), 3'ss of exon 4
-ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA
 | |||||||||  | | |   |  |  |      ||    |||||   | |    || |||  ||||| |  || ||||   ||||   |||  |   |||||||||||||||| ||||||||||| ||  | || || || || ||||||||||||||  |||| || |||||||||||||| || ||  |||| || |
gtaagctgtaatgcttatttggtagacaattccaggttccccagtagagt-taggactttgc--attttaa--tgtttcttcctgtccg-acatttcatagATAACTCACATGGAGATGATAAAAGGGATTCAAGGTCACGGATACTATGATGAACTTGTTGTCCCAATCATAGAGAACACAGCATATGAGAATGAACTAA

upper sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0014g02480.t01 (Vitis vinifera), 3'ss of exon 3
-ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA
 | |  | | |   |  ||    |   |||    | |||||  ||  | || | |  | |  ||   |||| ||  || || || | | || ||||| ||||| ||||| ||||||||||||||||||||  | || ||||||||||||||||| |||||| |||| || ||||||||||| ||| |||||   ||||| |
ataattttttacactttctagaatgtataataattctgttttggttctctgatatcttttaatttgcttgaattttttatgtttttgtgca-aaattacagATCACTCATATGGAAATGATAAAAGGAATTCAAGGACATGGTTATTATGATGAGCTTGTGGTCCCAATCATAGAGAACACTGCCCACGAAAGGGAGCTCA

upper sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ05771 (Selaginella moellendorffii), 3'ss of exon 1
ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA--------------------
                                                          |||  |  ||   | |||    |  | |   |||     | | |     ||||||| ||||| ||||||||||| ||||||||||| ||  |  | || ||  |||| || || || ||| | || || ||||||||| | |                    
----------------------------------------------------------tgcacagctt--ctggatctcagccggcgatacatcgcaccg-tcgtggacatggagatgatcaaaggaatcaaagggcatggttactaccactagctcgtagTCCCGATCATTGAAAACTCTGCGTATGAATATGAGGTCACGAATTCTATAGCAGCAGCC

upper sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34464 (Selaginella moellendorffii), 3'ss of exon 3
ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA
                                         | || ||| | ||| |||  || | || ||||||      |    |        || |||| ||||||||||| ||||| ||||||||||| ||||||||||| || || || |||||  |||| || || || ||| | || || ||||| ||||| |
---------------------------------------gtaatacttt-tctttttctctttttattcatttgagctccatctcgtgtggctgctgtagATCACTCACATGGAGATGATCAAAGGAATCAAAGGGCATGGTTACTACGACGAGCTTGTAGTCCCGATCATTGAAAACTCTGCGTATGAATACGAGCTCA

upper sequence: GLYMA06G36620.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ05817 (Selaginella moellendorffii), 3'ss of exon 3
ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA
                                                 ||  | || | ||| || |  ||| | |||  |   || ||     || |||| ||||||||||| ||||| ||||||||||| ||||||||||| || || || || ||  |||| || || || ||| | || || ||||| ||||| |
-------------------------------------------------gtaatacttttctttttctctttttactcttttgagctccatctgctgtagATCACTCACATGGAGATGATCAAAGGAATCAAAGGGCATGGTTACTACGACGAGCTCGTAGTCCCGATCATTGAAAACTCTGCGTATGAATACGAGCTCA

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|6502366|gb|AW203739.1|AW203739
EST:     TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAA                         ATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
genomic: TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAAgtaagcattt ... caaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
EST: gi|192334372|gb|FK024093.1|FK024093
EST:     TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAA                         ATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
genomic: TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAAgtaagcattt ... caaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
EST: gi|192331619|gb|FK022779.1|FK022779
EST:     TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAA                         ATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
genomic: TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAAgtaagcattt ... caaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
EST: gi|9565785|gb|BE475294.1|BE475294
EST:     TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAA                         ATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT
genomic: TAGAATCTTGTCTTGTAACAATGCTCAATCCTTTAGCAAAGGAATTTAAAgtaagcattt ... caaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA
                                       tcttcac  CT-rich tract
                ttattttgatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagctgtaattgtgactcattttattaaattgtgtgtttcagtaatttgtttttctctgcttattttgatttgattctggttgtcttcacaaattgcagATAACTCACATGGAAATGATAAAAGGAATCAAGGGGCATGGTTATTATGATGAACTTGTGATCCCCATAATAGAGAACACAGCCTACGAATATGAGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- agctgta
- - - - - - - - - - - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtcttca