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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttcatgttttttaattttcaattttgtttattgtctattgttttgagcttattataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG

Basic information

species Glycine max
transcript GLYMA11G10130.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G068913_T01 (Zea mays), 3'ss of exon 5
---------------------gtactgt--tcatgtttttta-attttcaattttgtttattgtctattgttttgagcttattataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
                     |  ||||   ||  || |  | ||  || ||||    | | | | |   | | |  ||||||  ||   |||  || || |||||||||| ||||||||||| || || |||||||| ||||| ||||||||  ||||||| ||     | ||   ||| |  |  ||||  |||||||||
gtattattctcttgctgctttgctctgtatccaaattatcaatatcatcgatttatcctgtggacaaagatgtagttcttatt-caatcgttcaattcatcagGTTGTAAACATGGAATGGGGCAATTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACGCAAAATCGCAATGATCAG

upper sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G20040.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------gtactgttcatgttttttaattttcaattttgtttattgtctattgttttgagcttattataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
                                                   |  ||| |  ||    |   ||||||||     | |   | || | ||     |  ||      |  | | | |||||| || |||||||| |||||||||||||||||||||| | | |||||||| || |||||  |||| || ||  | || ||    ||| |||||||   |
gtaataactattaagaatcgttacatagttcatccttagaaaccagccatcaaagtttagattccacaggattcaatttaaaagacttgattttttcttctttatgatactttgttattttgtgttagGTGGTCAATATGGAGTGGGGAAACTTTTGGTCATCTCGTCTGCCAAGAACTTCATATGACCTTGAGTTGGATGCAGAGAGTATGAATTCAAATGACATG

upper sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gtactgtt-catgttttttaattttcaattttgtttattgtctattgttttgagcttattataa---ctcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
       | |   || |||| | | |  ||   ||     ||||    | |  |      | |||  ||     | ||  | | | | |||| ||||||||||| |||||||| |||||||| |||||||| || ||||| || ||||| ||||| || ||  | || ||  | ||| ||||||||  |
gtactaagaatcattgcatggtctatttttagaaaccagctttagacccaaaagaaacatgtttaagattgattccctcttatgtttcagGTGGTAAATATGGAGTGGGGAAATTTTTGGTCCTCTCATTTGCCTAGAACTTCGTATGACATTGACTTGGATGCAGAGAGTTCAAATGCAAATGATATG

upper sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtactgttca-tgt-tttttaattttcaattttgtttattgtctattgttttgagcttattataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
                              |||    || ||  ||||| |   | ||   || || || | | |  | ||   |||  | | | |||||  ||  ||||||||| || |||||||||||||| || |||||||| ||||| |||||||||||||| ||||||||||||||   ||| || ||||||||||||||||||
gtatcctttcttgattttctagtcatacattacctaacactgcatttttgagaataaagactgattcttctatttattatttgacttcatgtca-tcttccattcgttagGTTGTCAACATGGAATGGGGAAATTTCTGGTCATCACATTTGCCAAGAACATCTTACGATATTGATTTAGATGGTGATAGTCCTAATCCAAATGATCAG

upper sequence: GLYMA11G10130.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S401_23V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gtactgttcatgttttttaattttcaat---tttgtttattgtctat-tgttttgagcttat--------tataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
         ||   |   |||  ||  |||||    |   ||||  ||||| | |  |    | |  | |         |||   || |    ||   ||||  | |||||||| |||||||||||||||||||| ||||| ||  | || | |   |||      || ||    || ||||   |||||   ||  | 
actgctctcgtgtaggatatgacttggaatttcgggtgggtttgaatattgaccacgtacccttacataacaagtgatatatggttcctgaccttggcagGTGATCAATATGGAGTGGGGAAACTTTTGGTCATCACATTTGCCTCGGACCTATGTGGATGAGTTATTGGATAGCGAGAGCCTCCATCCAGGAGAATAT

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|207848853|gb|GD818884.1|GD818884
EST:     TTGATGCTATTATCAAGTGTCAAGGTCTTCTTACAGCATCAGGATACATG                         GTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACA
genomic: TTGATGCTATTATCAAGTGTCAAGGTCTTCTTACAGCATCAGGATACATGgtactgttca ... tgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACA
EST: gi|207829107|gb|GD798097.1|GD798097
EST:     TTGATGCTATTATCAAGTGTCAAGGTCTTCTTACAGCATCAGGATACATG                         GTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACA
genomic: TTGATGCTATTATCAAGTGTCAAGGTCTTCTTACAGCATCAGGATACATGgtactgttca ... tgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattttgtttattgtctattgttttgagcttattataactcttctgtttattagGTTGTAAATATGGAATGGGGAAACTTTTGGTCATCTCATTTACCAAGAACATCTTATGATATTGATTTAGACTCTGAAAGCCCTAATCCAAATGATCAG
                                 ttataac  putative branch site (score: 2)
                                       ctcttctgtttatt  CT-rich tract
                              ttattataactctt  TA-rich tract