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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGACGAAACCCGTCACTCTGATTCAACAACTCTACGACGCCGGCCACCGATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaaaattacctttactcgtattttttatataaatttttttgaattgagattttataattaaaaataaaaatgcttcgttattttcgtcctttattgttagaaatttttagtaatttggttttggggcatgcctgcag

Basic information

species Glycine max
transcript GLYMA08G43230.3
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G43230.3 (Glycine max), 5'ss of exon 1
lower sequence: LOC_Os01g72205.1 (Oryza sativa), 5'ss of exon 1
CAAGACGAAACCCGTCACTCTGATTCAACAACTCTACGACGCCGGCCACCGATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaaaattacctttactcgtattttttatataaatttttttgaattgagattttataattaaaaataaaaatgcttcgttattttcgtcctttattgttagaaatttttagtaatttggttttggggcatgcctgcag
 |||||||| || ||  |  || | |   | |||||||||||||||||||| | ||||||||| ||||||||||| ||  || ||   || || || ||||| | |   |  ||   |||  ||||   |||       | |        | || |     | | |        |     |  |  ||| | |                                                   
GAAGACGAAGCCGGTGTCGATGGTGCGGGAGCTCTACGACGCCGGCCACCGCTGCTTCGGCGAGAACTACGTCCAGGAGTTCGTCACCAAGGCGCCGCAGgttcgg---agtttgattttcttcgtggattt---gcggaatccgccatttggaaacgacttgacttgtggctgattgattctgccattgttgcag------------------------------------------------

upper sequence: GLYMA08G43230.3 (Glycine max), 5'ss of exon 1
lower sequence: Vv19s0090g00910.t01 (Vitis vinifera), 5'ss of exon 1
CAAGACGAAACCCGTCACTCTGATTCAACAACTCTACGACGCCGGCCACCGATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaaaattacctttactcgtattttttatataaatttttttgaattgagattttataattaaaaataaaaatgcttcgttattttcgtcctttattgttagaaatttttagtaatttggttttggggcatgcctgcag
 || || ||||| ||| |||| || |  ||| ||||||||||||| ||||| |  || |||||||||||||| ||||| || | ||||||||| || |||||    | | |  |   |  ||| |  | | | || || || |                                                                                                     
AAAAACCAAACCAGTCTCTCTCATCCGGCAAGTCTACGACGCCGGTCACCGTTGTTTTGGCGAAAACTACGTTCAAGAGATAAACGAAAAAGCACCACAGgtctctctataggt--ttgcacttgcgtatgt-atgtatatgtnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn-----------------------------------------
















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|298199617|gb|HO043494.1|HO043494
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|209708248|gb|BW678618.1|BW678618
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|120530250|gb|EH258384.1|EH258384
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|20498376|gb|BQ273306.1|BQ273306
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|209728275|gb|BW658487.1|BW658487
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|21285679|gb|BQ473550.1|BQ473550
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|298165006|gb|HO011055.1|HO011055
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|20207929|gb|BQ134018.1|BQ134018
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|298163042|gb|HO011775.1|HO011775
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|298179673|gb|HO024888.1|HO024888
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|20449854|gb|BQ253978.1|BQ253978
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|15664325|gb|BI701696.1|BI701696
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|10843789|gb|BF067045.1|BF067045
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|209705383|gb|BW668013.1|BW668013
EST:     GATACTTTGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|7926422|gb|AW832448.1|AW832448
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|21993868|gb|BQ785396.1|BQ785396
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|15337855|gb|BI498511.1|BI498511
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|17401932|gb|BM178714.1|BM178714
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|15285565|gb|BI469456.1|BI469456
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA
EST: gi|20207556|gb|BQ133645.1|BQ133645
EST:     GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAG                         CTTCCTCAAGACGTTGAATGGCATTTCATTGGGCATTTGCAAAGCAACAAA
genomic: GATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaa ... atgcctgcagCTTCCTCAAGACGTTGAGTGGCATTTCATTGGGCATTTGCAAAGCAACAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGACGAAACCCGTCACTCTGATTCAACAACTCTACGACGCCGGCCACCGATACTTCGGCGAAAACTACGTCCAAGAAATCATCGAAAAAGCTCCTCAGgtgctgcaaaaattacctttactcgtattttttatataaatttttttgaattgagattttataattaaaaataaaaatgcttcgttattttcgtcctttattgttagaaatttttagtaatttggttttggggcatgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC