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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacttctttgtttctcatgcgcgctttcattttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG

Basic information

species Glycine max
transcript GLYMA10G05610.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G05610.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ24973 (Selaginella moellendorffii), 3'ss of exon 1
gtacacttctttgtttctcatgcgcgctttcattttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG
                         |     |||  | |   ||| ||    |   |||     |||   |    |  |  ||  |||||| || || ||||| || ||||||||||||||||| ||||| ||||| || ||||| ||||| |||| |||  | || |||||||||||  | || || 
-------------------------gtaagtattgctggaa-gttctttcgatcctttgtggtgatactatcttcttctactttgcagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT

upper sequence: GLYMA10G05610.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15374 (Selaginella moellendorffii), 3'ss of exon 1
gtacacttctttgtttctcatgcgcgctttcattttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG
                            |   | ||   |   |  || | | | ||    | ||  |  | | |   |  ||   ||||| || || ||||| || ||||||||||||||||| ||||| ||||| || ||||| ||||| |||| |||  | || |||||||||||  | || || 
---------------------------gtaagtattgcttcgatcctttgtggtgat---gttaactatcttcttc--tactttgtagAGCCAGTGACAAGTGCCAAAGAGAGAAGAGGAAGACGATCAATGGCGATGACTTGCTATGGGCAATGAGCACGCTGGGCTTCGAGGAGTACTTGGAACCT
















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|31469579|gb|CD411607.1|CD411607
EST:     GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGA                         AGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
genomic: GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGAgtacacttct ... tgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
EST: gi|298187763|gb|HO031720.1|HO031720
EST:     GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGA                         AGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
genomic: GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGAgtacacttct ... tgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
EST: gi|298196414|gb|HO041157.1|HO041157
EST:     GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGA                         AGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
genomic: GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGAgtacacttct ... tgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
EST: gi|16341802|gb|BI967397.1|BI967397
EST:     GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGA                         AGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
genomic: GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGAgtacacttct ... tgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
EST: gi|298197939|gb|HO039478.1|HO039478
EST:     GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGA                         AGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA
genomic: GAAACCGTGCAGGAATGCGTCTCCGAGTTCATCAGCTTCGTCACCAGCGAgtacacttct ... tgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG
                 cgttaat  putative branch site (score: 4)
                   ttaattgaatgaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacttctttgtttctcatgcgcgctttcattttttgtttgttattcgcgttaattgaatgaataaattgcgttgttgtttaacagAGCGAGCGATAAGTGTCAGAGAGAGAAGAGGAAGACCATCAACGGCGACGATTTGCTTTGGGCTATGACCACTTTAGGTTTCGAGGAGTATATTGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG