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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtttcttaatttttcttatgttggatgttttgacaaactcaaatacttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA

Basic information

species Glycine max
transcript GLYMA06G11860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g07110.1 (Oryza sativa), 3'ss of exon 5
gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtttcttaatt--tttcttatgttggatgttttgacaaactcaaatacttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA
                                                  | || | || | |    | || || | | ||   || |||| | |  ||   |      |     ||  || ||| ||    | || || |||||||| | ||  |||||||||||||| || |||||  | ||||||||||||||||||||||||||||| | || ||| ||| |  
--------------------------------------------------gtgactctaaaatagcatctatttacatcatcggttacttaagattaataactcactgtat--ggatttttttttcagGCACTCATAGCTGCTGTTGGGGCTTCCATAGGATATGGATCACCCTTGACCCTGACTGATACATCAAACAAAATAAAAAAGGGAACACTGGGTGATGCTT

upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G118286_T01 (Zea mays), 3'ss of exon 5
---------------------------gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtt-tcttaatttttcttatgttggatgttttgacaaactcaaatacttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA
                             |    | |  |||  | || ||   |||||  |  |   |||       |  ||| |  |    |   |  | | ||  ||| |  |||  |   | ||    ||    |||||||||  |||||    | || || |||||||| |  |  |||||||||||||| ||||||||  | | ||||||||| || |||||||||||||| |  |  || ||| |  
gtagctttcaatcggcaacaaaatgggtcaaatctgttcactatattgtattttttgaaagacaagggcaggagctctgacattcatttaagataggaactatattggtttattatataatctttattc-atcatttgcaaatactt--tttagGCACTAATGGCTGCTGTTGGGGCCTCAATAGGATATGGATCACCTTTGACCCTGATTGATACATCCAATAAAATAAAAAAGGGAACTCTAGGTGATGCTT

upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G117064_T01 (Zea mays), 3'ss of exon 3
gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtttcttaatttttcttatgttggatgttttgacaaactcaaatacttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA
                                      |     || | | || ||     || | ||  |  || ||  | ||| ||||| ||      || |   |  |||||      |||||    | ||  | | |||||| | ||  ||||| || || || ||||||||  | |||||||||||||| ||||||||||||||||  || || ||| |  
-------------------------------------gtaagcattgacatggcatgccagtt-tattccacattgttgttcttttttatgctga----cttaatctatgcaaatggaatgtttagGCAATCATAACTGGTGTTGGGGCTTCAATAGGTTACGGGTCACCTTTGACCCTGACTGATACATCAAATAAAATAAAAAAGGGGACGCAAGGTGATGCTT

upper sequence: GLYMA06G11860.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G77590.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgggtttctacttcagtgaatggattgaataaatatttcagtttaaagggaatttagattgtgttttagtttcttaatttttcttatgttggatgttttgacaaactcaaatac--ttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA
                                          |  ||||| |    |||     ||  ||  | |   | ||   |   |   |  | |||  |      | ||| |  ||||| ||||   | || ||  || ||||  ||  ||| |||||||| ||||| |||||  |||| ||||| |||||||| ||||||||||| | | | || |||  ||
----------------------------------------gtatcttaaaagttcattactcaatgcgtttatatagcagttccacac-ttcagagtatttgaatgcggcctaattccattgttgtagAGCGTAATGGCTACTATTGGGAGTGCTATTGGATATGGGTCTCCCTTGACGCTAACGGATACTTCAAACAAGATAAAAAAGGGTACAAAAGGAGATGTCA

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|7030305|gb|AW460088.1|AW460088
EST:     TCTATCTAGCATACTTACCGATGGCTCATATCCTTGAATTAGTAGCTGAG                         AATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACT
genomic: TCTATCTAGCATACTTACCGATGGCTCATATCCTTGAATTAGTAGCTGAGgtatgggttt ... cttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttaatttttcttatgttggatgttttgacaaactcaaatacttgttttagAATTTGATTGCAGCTGTTGGAGGTTGTATAGGATATGGATCTCCTTTGACTTTAACTGATACATCAAACAAAATAAAAAAGGGGAAACAGGGGGATTCCA
                           ttttgac  putative branch site (score: 3)
                                             cttgtttt  putative PPT
     ttaatttttcttatgt  TA-rich tract