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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

taagctttgtaaaaatatcacaaatgcatattttcccttctatattcgatcacattacaaactttattttgtggtggtcttagtcttactttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG

Basic information

species Glycine max
transcript GLYMA18G12830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g47470.1 (Oryza sativa), 3'ss of exon 3
taagctttgtaaaaatatcacaaatgcatattttcccttctatattcgatcacattacaaactttattttgtggtggtcttagtcttactttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG--
                                                                          |||   |  | || |||   ||||  | |||     ||  |  | |||||||||||   | |||  |     | |||  | |       ||     | |  |||||| |||| || ||||||||||| |||||||| ||| ||||||||||||| |||||||| |||||       || |  ||||| ||||||   || |||||    
-------------------------------------------------------------------------atggaaattctgttccttcccttgtgcataat-----caatatgtgttttccttgttcccttgtttctcactgtacat--tgaccttttctgaatattcacctgcagGATGCTTGTCTATGAATATGTCAACAATGGAAACCTAGAACAATGGCTTCATGGGGCCATGAGTGGG---GGCATCCTTACTTGGGAAAACCGTATGAAGATT

upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 3
taagctttgtaaaaatatcacaaatgcatattttcccttctatattcgatcacattacaaactttattttgtggtggtcttagtcttactttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG
                                                                   || |||||       |||  | | ||| | |        || |||  | |   | |  ||||  | || ||    |||  || ||  |  ||   |||   | |    | |||| |||| || || |||||||| || || || ||||||||||| ||||| ||||| || ||| ||||||| ||    |||||||||||||| ||||||||| 
-------------------------------------------------------------------ttagtggttagtggtgtccaaatctttctttg-------tgtacatcatactatgtttttgtagtcta-ttaaacttccatcctatcatctg-acttgttatat----tccagGATGCTTGTATACGAATATGTGAATAACGGGAACTTAGAACAGTGGCTTCATGGTGCCATGCGCCAACATGGTGTTCTTACCTGGGAAGCCCGAATGAAA-

upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 2
taagctttgtaaaaatatcacaaatgcatattttcccttctatattcgatcacattacaaactttattttgtggtggtcttagtcttactttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG
                                                                                                               ||     ||| || ||  |  ||        ||   |  || | |||     |    |      |||||| |||| || ||||| ||||| || | ||||||||||||||||||||||||||| || ||| | ||||| || |  || || |||||||| || |||||| 
------------------------------------------------------------------------------------------------------------gtgagtctcacttgtctttaatccatttgagcaattggattgtactgaatctaaatataatgatgaatgcagGATGCTTGTTTATGAGTATGTTAATAGTGGTAACTTAGAACAATGGCTACATGGAGCAATGCGGCAACATGGAAATCTCACTTGGGAAGCACGGATGAAA-

upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
taagctttgtaaaaatatcacaaatgcatattttcccttctatattcgatcacattacaaactttattttgtggtggtcttagtct--tactttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG
                                                         |  ||||  | |  |    |||| | | |  ||||  ||| |||  |    |||  |        ||    |     ||||    || ||     ||  || | | |||    | | |  |||||| |||| || ||||| ||||| || | ||||||||||||||||||||||||||| || ||| |  ||||| | || || || ||||| ||||| |||||| 
---------------------------------------------------gtgagtctgactt-gtctcttatcagtctgaatgtactactaatttagtctca----tgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgtaa--tgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA-

upper sequence: GLYMA18G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
-taagctttgtaaaaatatcacaaatgc---atattttcccttctatattcgat---cacattacaaactttattttgtggtggtcttagtcttac-tttttttgtcaaaaatttgaacagaacatcttttccttgttatatagttctttttctttcataataaatgcggttgccgtctgatt---------tgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG
 |||| |||||  |  | | |   |||    |  || |  | |   |||||  |   ||  ||  |   | |  ||  |  | ||| |  |       ||||| ||  ||||    |  |      |  ||| ||   |      ||  | |  ||        ||| ||||     || |||         |  ||| ||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| |||||| ||||| | || |  ||||| ||||| || || |||||  
gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaagtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAG-

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|18730090|gb|BM525675.1|BM525675
EST:     ATAAAAATCTTGTGCGCTTACTTGGTTATTGCGTAGAAGGAGTTCACAGG                         TTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACAT
genomic: ATAAAAATCTTGTGCGCTTACTTGGTTATTGCGTAGAAGGAGTTCACAGGtaagctttgt ... gatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACAT
EST: gi|192331429|gb|FK019902.1|FK019902
EST:     ATAAAAATCTTGTGCGCTTACTTGGTTATTGCGTAGAAGGAGTTCACAGG                         TTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACAT
genomic: ATAAAAATCTTGTGCGCTTACTTGGTTATTGCGTAGAAGGAGTTCACAGGtaagctttgt ... gatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttatatagttctttttctttcataataaatgcggttgccgtctgatttgcaggTTGCTGGTGTATGAATATGTAAACAATGGTAACTTAGAACAATGGCTACATGGGGCTATGAGCCAACAAGGGACACTTACCTGGGAAGCTCGAATGAAAG
                                         gtctgat  putative branch site (score: 4)
     tatagttctttttctt  TA-rich tract