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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaattacctgtctactaagtgttgcttctctttccttgtctcccctgtcttactctctccagcatcaaatcttaatttgagctttatctttttacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATGTTTGTGGTAGGAGTGAATGAGAAGACATACAACCCAAAAATGGACATTG

Basic information

species Glycine max
transcript GLYMA16G09020.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 7
gtatccaattacctgtctactaagtgttgcttctcttt-ccttgtctcccctgtcttactctctccagcatcaaatcttaatttgagctttatctttttacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATGTTTGTGGTAGGAGTGAATGAGAAGACATACAACCCAAAAATGGACATTG
              || |    |   || ||   | || || | |  |       |  |   ||     ||   ||   |   |||  ||| | |   |    ||||||  ||||| ||||||||||| ||||| |||||||| |||||||| ||||||||||| || ||||| ||||||||||  ||  | || |||||| |  |||
--------------gtttgtacaccatttctatacattgccatctaactgagaaatggcaagcttttatattggataaaatggtgatgtttttatgccttgtttgtagGGCGGTGCTAAGAAAGTTGTGATATCTGCTCCATCAGCAGATGCTCCAATGTTTGTCGTTGGAGTAAATGAGAAGAGCTATGATCCTAAAATGAATGTTG

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G090808_T01 (Zea mays), 3'ss of exon 2
----gtatccaattacctgtctactaagtgttgcttctctttccttgtctcccctgtcttactctctccagcatcaaatcttaatttgagctttatctttttacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATGTTTGTGGTAGGAGTGAATGAGAAGACATACAACCCAAAAATGGACATTG---------
    || |  |      |   | ||||   | || ||   ||   | ||| |    ||||    | || |  |    || || || |     || | ||||||||     || |||||| |||||||| || |         ||||||||||||| ||||||||||| || ||||| |||||||| |  ||  | ||||| ||| |  |||         
gtttgtgtgtaccagaataatttctaacaatggcatccaattaactatctgcag-atcttttcgtatcgaaaac---atgttgatgtttctgttgtttttttaca-----gGGTGGTGCTAAGAAAGTGGTGA---------CATCTGCAGATGCTCCAATGTTTGTAGTTGGAGTTAATGAGAATAGCTATGATCCAAAGATGAATGTTGTTTCTAATG

upper sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 7
gtatccaattacctgtctactaagtgttgcttctctttccttgtctcccctgt---cttactctctccagcatcaaatcttaatttgagctttatctttttacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATGTTTGTGGTAGGAGTGAATGAGAAGACATACAACCCAAAAATGGACATTG
              || |  ||  |||||      ||   ||   ||  ||     ||  ||  |  |  ||         | |  | | ||    | |||| | || ||| ||||||||||||||| ||||| ||||||||||| || |||||||| ||||||||||||||||| |||||||   ||||||| ||||  ||| | ||||
----------gttcgt-tggtatatgttgtggactttatattagttcttctaaacactctcttgccaccccactgtgctgaagtcagtgattgtcgtctttataatgcagGGTGGTGCCAAGAAAGTGGTAATTTCAGCTCCATCAGCTGATGCACCGATGTTTGTGGTAGGAGTAAATGAGACTTCATACAAGCCAAGCATGAATATTG

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|254326010|gb|GR838891.1|GR838891
EST:     AGTCTTCTGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG                         GCTGGTGCCAAGAA-GTTGTAATATCAGCTCCATCTGCAGATGCACCAATG
genomic: AGTCTTCTGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAGgtatccaatt ... tacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATG
EST: gi|254346561|gb|GR856283.1|GR856283
EST:     AGTCTTCTGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAG                         GCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATG
genomic: AGTCTTCTGGAGTTTTTACAACAGTGGAGAAAGCTTCATCACATTTGAAGgtatccaatt ... tacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttactctctccagcatcaaatcttaatttgagctttatctttttacactgtagGCTGGTGCCAAGAAAGTTGTAATATCAGCTCCATCTGCAGATGCACCAATGTTTGTGGTAGGAGTGAATGAGAAGACATACAACCCAAAAATGGACATTG
                      tcttaat  putative branch site (score: 3)
                                  ctttatctttttac  putative PPT
                atcaaatcttaattt  TA-rich tract