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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgggaggtgtgataagatccctcctcatctggtttattaaatataattgtatgatgttgaattccgtatttagatctattgactggtcaaaataaaaaaattggttttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG

Basic information

species Glycine max
transcript GLYMA01G41600.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 7
gtaatgggaggtgtgataagatccctcctcatctggtttattaaatataattgtatgatgttgaattccgtatttagatctattgactggtcaaaataaaaaaattggttttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG
                                                            || |  |  ||| || | ||   | |  |    ||||  | |||   |||| | ||   ||   |   | ||    |||  || ||  |  |  |    |  ||||  |  ||||||| || |||||    || ||||| || ||||||||||| |||||||| || || |||||||| ||||||||||| ||||| || | ||
------------------------------------------------------------ttaatatttgtactttgttcatctaaaagaattaaattgataaacgagtttaactt---tttgctaccaatgacaagtggctaatggtctataatggt-tacagGTCCTCAATTACAAGACTCAGCAAAGCAGACTCTTTCCTTTGCTGGCTTCAGCTTATGCATTTAGGTTTGTGGGTGAGTGGCTGAAGTGGCTGTACACGG

upper sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 7
gtaatgggaggtgtgataagatccctcctcatctggtttattaaatataattgtatgatgttgaattccgtatttagatctattgactggtcaaaataaaaaaattggttttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG
                                                             |||| ||  | ||  ||   |  ||   ||  |  |  |   ||   || |      | |   |   | ||    |    || |||   |    |   |  ||||  || ||||||| || || |||   || ||||| |||||||||||||| || ||||| || ||||||||||| || ||||| || ||||| |||| ||
------------------------------------------------------------gtgaagtcttt-ttgggacggaggga---gtacatgtgcatggatgcattctgcaacttctagctaccaatgagaggcaactaatgtattgaaactgattacagGTCCTTAATTACAAGACTCAACAGAGCAGACTCTTTCCATTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGATTGGCTCAACTGGCTATATACGG

upper sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G864319_T01 (Zea mays), 3'ss of exon 7
gtaatgggaggtgtgataagatccctcctcatctggtttattaaatataattgtatgatgttgaattccgtatttagatctattgactggtcaaaataaaaaaattggttttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG
                                                             | || | |      ||   ||    |||  |  || |   ||| ||  | |  |  ||| |   | ||  ||  |   | ||||    | |  || ||    |||  |||||||||| || || ||    || ||||| || ||||||||||| || ||||| || ||||||||||| || |||||||| ||||| || ||||
----------------------------------------------------------gaatcaactgcccgcccagtgttaccacctgtgcttaacatggaaaatgcatctg-tcggttaccaacaaaaggtgtctaacatatt-caagctggttaca----gGTCCTTGATTACAAGACTCAACAAAGCAGACTCTTTCCGTTGCTGGCTTCAGCATATGCATTTAGATTTGTGGGTGACTGGCTGAAGTGGCTATACATGG

upper sequence: GLYMA01G41600.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv00s0389g00020.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgggaggtgtgataagatccctcctcatctggtttattaaatataattgtatgatgttgaattccgtatttagatctattgactggtcaaaataaaaaaattggttttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG
                                                              ||  ||     ||   |  | ||  |  ||||||| |||  | |  | |||  |      |   |     ||  |   ||  |||    ||  ||  |||||||||||||||||||||| |||||   ||||||||| || |||||||||||||| ||||||||||||||||| ||  ||||| |||||||||| |||||||
------------------------------------------------------------gagatatctagggttttctgcagtggattttcaaaattaaatcact--tcttagctctaaagaagatgtaattaatggattttctgtttacttggtc--tttagGTGATTGATTACAAAACTCAGCAAAGTAGGCTCTTTCCTTTGCTGGCTTCTGCCTATGCTTTCAGATTTGTTGGTCAGTGGTTGAAATGGCTATATATGG

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|16349011|gb|BI974606.1|BI974606
EST:     GTGCTGTTAGAAGACAGTTTGGATCACATAATGGAGGTCTAGAAACACAG                         GTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCT
genomic: GTGCTGTTAGAAGACAGTTTGGATCACATAATGGAGGTCTAGAAACACAGgtaatgggag ... ttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCT
EST: gi|105635049|gb|DW247750.1|DW247750
EST:     GTGCTGTTAGAAGACAGTTTGGATCACATAATGGAGGTCTAGAAACACAG                         GTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCT
genomic: GTGCTGTTAGAAGACAGTTTGGATCACATAATGGAGGTCTAGAAACACAGgtaatgggag ... ttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattagtttcattctaagtgtagcgtgcttattgtgcggtttttccatttagGTGATTGATTACAAAACACAGCAGGCTAGGCTCTTCCCATTGCTGGCTTCTGCTTATGCTTTCAGATTTGTGGGCGAGTGGCTGAAATGGCTTTATATGG
 ttttaat  putative branch site (score: 3)
                                          tttttccattt  putative PPT
     ttagttt  TA-rich tract