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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgatttaaatttgctgctaacttttttttactaccctactttcatcgattataagttttctgtttgtccatttttctgtaattaagatttaaat...

Basic information

species Glycine max
transcript GLYMA01G39330.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39330.1 (Glycine max), 5'ss of exon 12
lower sequence: AT4G36960.1 (Arabidopsis thaliana), 5'ss of exon 11
TAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgatttaaatttgctgctaacttttttttactaccctactttcatcgattataagttttctgtttgtccatttttctgtaattaagatttaaat
 |||||||  || ||||||||||||||||||||||| ||||||||| ||||||| |||||||| ||  | ||||| |||||||| || ||||||||  |||||  |  |   ||  ||| | ||   |  |||  || |       |  |     |||||     ||       || | || ||   ||  | ||||   
AAAGAGAAGTGGACATAGAGGTTTTGGATTTGTTACCTTTGCTGAAAATGGTGTTGCAGATCGTGTAGCCCGAAGATCTCATGAAATCTGTGGACAAGAGgtaaaaaaac--aagcttgatacttgatgctttagacaaaaacttatctaagatgtataaagaagcta------cactgttttgattttcgggtttag--

upper sequence: GLYMA01G39330.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv07s0031g00600.t01 (Vitis vinifera), 5'ss of exon 12
TAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgatttaaatttgctgctaactttt-ttttac-taccctactttcatcgattataagttttct---gtttgtccatttttctgtaattaagatttaaat
||||||||  || ||||| || ||||| ||||| || |||||||||||||||||||| ||||| || ||||||||||||||||||||||| ||||| |||||| |   ||  ||  ||  || | | |||| |||||| |||   | | |||| |||  | |   || |   |||||   || | | ||| | | | ||      
TAAGAGAAGTGGCCATAGGGGCTTTGGTTTTGTAACCTTTGCTGAAGATGGTGTAGCTGATCGTGTATCTCGAAGGTCTCATGAGATTTGCGGACAGCAGgtatggaaatggaagcttaatggtcatttttgttttacctacataattatcatagatcttgaaagttataaagtttggtgatgtctatgtcactgatata-----
















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|58020024|gb|CX706766.1|CX706766
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|193512455|gb|FK467273.1|FK467273
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|58023593|gb|CX710334.1|CX710334
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|254318602|gb|GR832770.1|GR832770
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         -TGGCA-TAGATTCG-CTACTC-TGTTGATGATGCAGG-CCCAGTGGGA-T
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|13790928|gb|BG653519.1|BG653519
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|58024913|gb|CX711654.1|CX711654
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|209710036|gb|BW658864.1|BW658864
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|254337734|gb|GR845304.1|GR845304
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|58020404|gb|CX707146.1|CX707146
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
EST: gi|18711451|gb|BM522593.1|BM522593
EST:     GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAG                         GTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT
genomic: GTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgat ... gcacctgcagGTGGCAATAGATTCGGCTACTCCTGTTGATGATGCAGGGCCCAGTGGGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGAGAACAGGTCATAGAGGTTTTGGATTTGTTACTTTTGCTGAAGATGGTGTAGCAGATCGCGTCTCTCGAAGGTCTCATGAGATTTGTGGACATCAGgtacgatgatttaaatttgctgctaacttttttttactaccctactttcatcgattataagttttctgtttgtccatttttctgtaattaagatttaaat

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT