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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaattctaactcataagtttccaagtcatgtatttgcatgtgcagcttgttcgtgttaatctaatgtttgttgtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAACAAGCTTGCTAAACATCTTCGCAGCATTGAGTCTATTGTTATAGCCAAGA

Basic information

species Glycine max
transcript GLYMA11G20630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20630.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g02890.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------gtacaattctaactcataagtttccaagtcatgtatttgcatgtgcagcttgttcgtgttaatctaatgtttg-ttgtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAACAAGCTTGCTAAACATCTTCGCAGCATTGAGTCTATTGTTATAGCCAAGA
                          ||    ||| | || |||| | ||||  |||  | | || |  |     || |  |  | | ||| || | || ||| ||||  |||| ||||| || |||||||| || ||||||||||| || |||||||| ||||||||||| |||||||| |   ||||||||||| ||||||||||||| |
gtatcatttcattcctagtaataagtgtgtgcttccatct-ataattctccatctca-atttctgtactt-----ttatgggaataattctgatatgtgcttggaatac-agATCTATGCACCATGGTGTGGTCATTGCCAAGCTCTTGAGCCAACATATAACAAGCTTGCCAAACATCTACATGGCATTGAGTCTCTTGTTATAGCCAAAA
















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|151395537|gb|EV265414.1|EV265414
EST:     ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
EST: gi|298187911|gb|HO031868.1|HO031868
EST:     ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
EST: gi|22928956|gb|BU546095.1|BU546095
EST:     GTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCNCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
genomic: GTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
EST: gi|298173403|gb|HO016739.1|HO016739
EST:     ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
EST: gi|9821020|gb|BE556530.1|BE556530
EST:     ATAACTTTGATGAAATTGACTTGGATGAGTCAAAGGATGTTCTGCTAGAG                         ATATATGCTGCCTGGTGTGGCCACTGCGCA-GCTCTGGAACCA
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGC-CAAGCTCTGGAACCA
EST: gi|7796807|gb|AW782201.1|AW782201
EST:     ATAACTNTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCCC
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCC
EST: gi|151403024|gb|EV272837.1|EV272837
EST:     ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCCCCGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
EST: gi|6567046|gb|AW234673.1|AW234673
EST:     ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAG                         ATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC
genomic: ATAACTTTGATGAAATTGTCTTGGATGAGTCAAAGGATGTTCTGCTTGAGgtacaattct ... gtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtatttgcatgtgcagcttgttcgtgttaatctaatgtttgttgtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAACAAGCTTGCTAAACATCTTCGCAGCATTGAGTCTATTGTTATAGCCAAGA
                               atctaat  putative branch site (score: 3)
                                       tttgttgtaatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaattctaactcataagtttccaagtcatgtatttgcatgtgcagcttgttcgtgttaatctaatgtttgttgtaatattagATTTATGCTCCCTGGTGTGGCCACTGCCAAGCTCTGGAACCAACATACAACAAGCTTGCTAAACATCTTCGCAGCATTGAGTCTATTGTTATAGCCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT