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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagtttgaagcagttttttgtgtggttgcttttttttttccgttggcatctcagtttatcagcaagactcgttaatatttttattgtttggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAGAGAGAAAGGCGTGTTGTATTTAGAAAAGCATGATAAATCTATGCTTTAC

Basic information

species Glycine max
transcript GLYMA17G11220.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 16
acagtttgaagcagttttttgtgtggttgcttttttttttccgttggcatctcagtttatcagcaagactcgttaatatttt--tattgtttggtt-ttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAGAGAGAAAGGCGTGTTGTATTTAGAAAAGCATGATA-AATCTATGCTTTAC
                      |||       | |  |     |||  || | | |   | |   ||  || ||  | || |  ||   || || |  | |||||| ||||||| ||| | ||||||||||| || |||||| | ||||||||||||||  | | |||  |  |  | || || |||    | || ||   || 
----------------------gtgaggaacctgtcatactatttgctatttaattaattgatttagtatcatttttcttatgctaccattcggctgcttcagGTGCGAAGAGCCCTTCTGATCATGCACCAAAGGGATGAAGTGGAGTACAAGAGAGAGCGCCATGTCATTGTCCGGAAGGCTTGAGGTGAACTGTGGAGTA-
















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|208062842|gb|GD861130.1|GD861130
EST:     AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
genomic: AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
EST: gi|208087550|gb|GD886884.1|GD886884
EST:     AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATT                         GTGAGAAGAGCTCTTATAATCACGCACCAGAGAGATGAAATAGAGTACAAG
genomic: AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
EST: gi|22932051|gb|BU549190.1|BU549190
EST:     AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
genomic: AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
EST: gi|208315884|gb|GE114828.1|GE114828
EST:     AGCAGAATGGGGTATTGTAATTGTAATCTATT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAA
genomic: AGCAGAATGGGG-A-TG-AA-TG-AATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAA
EST: gi|208280666|gb|GE075880.1|GE075880
EST:     CAGAATGGGGATGAATGAATCTATTT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAA
genomic: CAGAATGGGGATGAATGAATCTA-TTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAA
EST: gi|18717775|gb|BM522997.1|BM522997
EST:     AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
genomic: AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
EST: gi|208028836|gb|GD828750.1|GD828750
EST:     AAGAAGGCTGATTGATGACCTCAGCAGAAGTGGGGATGAATGAATCTATT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
genomic: AAGAAGGCTGATTGATGACCTCAGCAGAA-TGGGGATGAATGAATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG
EST: gi|208066187|gb|GD863984.1|GD863984
EST:     AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATT                         GTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAGTAGAGTACAAG
genomic: AAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagttcca ... ggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcatctcagtttatcagcaagactcgttaatatttttattgtttggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAGAGAGAAAGGCGTGTTGTATTTAGAAAAGCATGATAAATCTATGCTTTAC
                         cgttaat  putative branch site (score: 4)
                           ttaatatttttattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acagtttgaagcagttttttgtgtggttgcttttttttttccgttggcatctcagtttatcagcaagactcgttaatatttttattgtttggttttgcagGTGAGAAGAGCTCTTATAATCATGCACCAGAGAGATGAAATAGAGTACAAGAGAGAAAGGCGTGTTGTATTTAGAAAAGCATGATAAATCTATGCTTTAC

- - - - - - - - - - - gtggttg