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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA

Basic information

species Glycine max
transcript GLYMA17G36230.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G36230.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g10820.t01 (Vitis vinifera), 3'ss of exon 1
--------------------ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgtttttttta-ttgttcatcttataattttgaaaaccctaatttgtgtgta-
                        |  ||||  |||| |||      |||   |||    || ||||  |||||| |  |   |  ||    || ||||  || |  | ||   |        ||| |  ||   || ||||||||||| || |||||||| |||||||||||| |||| |||||||| ||||||||||| ||||| || || |||||||| |||||||| |||| 
gtaacatcttgacgccaagacaagttttatttcaatt-ttagggctgctttgtgatttttttattcgcatcacttccaaaccctaattagggtttttcaatttgttttcttttgatttggggattgggaataatagGGAGAGCTGGAGTTCCCATGGAAGTCATGGGTCTGATGCTGGGAGAGTTCGTTGATGAGTACACAGTTCGTGTAGTAGATGTGTTCGCGATGCCGCAGAG

upper sequence: GLYMA17G36230.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 3'ss of exon 2
ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA-
         ||    ||| | |||  | ||||   |   | |    || |  || |  |||| ||    || | |   | | |     ||   |      |  | | || ||| |||||||||||||| ||||| |||||||| |||||| | | |||||| || ||||| ||||| ||| | |||||| ||||||| || |||||||| | 
---------tttaccttcgt-tttcatgttcttatttgtcctggaggtct--ctcttgcatgattacagtagtataattttaacctggtttcgattttggacatatctgcagGTAGAGCTGGAGTACCCATGGAGGTGATGGGGCTGATGCTTGTGGAGTTTGTTGATGAATACACAGTTTGTGTTGTGAATGTGTTCGCTATGCCTCAAAG

upper sequence: GLYMA17G36230.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S146_35V6.1 (Physcomitrella patens), 3'ss of exon 1
ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA-
            |  || | |  ||    | |  |  ||    | |  |   |  |  | || || |      ||| || |       ||  |  ||   |  |  ||| ||| ||||| ||||| || |||||||||||||| |||||| | |||||||| ||||| |||||||| ||||| || || ||||| ||||| |||||||||| 
-----------tgttttttcacgtttggctatgtacacctagatgcaatat-ccctttcgtgcttatcaggaggttgatttgcactggtttcatgcctggacgttcgtgcagGTAGAGCGGGAGTTCCTATGGAAGTGATGGGACTGATGCTCGGGGAGTTTGTGGACGAGTACACTGTTCGTGTCGTAGATGTATTTGCTATGCCTCAGAG

upper sequence: GLYMA17G36230.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA-
    | | |||||  |||    | | |  |||  |     |   |   ||    |||    |      ||    |  |  |  | |      |||     |     ||| ||| ||||||||||| || ||||| |||||||| |||||| | |||||||||||||| |||||||| ||||| ||||||||||| ||||| ||||| |||| 
----tac-attagggttc--ggtctattgtctaaagaatttaaatgacttgctcttcgttgggagggcttggattcaaattggtgac-----aaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG

upper sequence: GLYMA17G36230.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37436 (Selaginella moellendorffii), 3'ss of exon 1
ggtatgctattagaattcttattttctcttctcgatccccttcttcgtttcactttcccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA-
                                                 | |         |   |    ||| ||| |  || |  ||||          ||  |  | ||| ||||||||||| || |||||||| ||||| |||||| | ||||| || ||||| |||||||| |||||||| ||||| || |||||||||||||||| 
------------------------------------------------gtaaggagggagagagctccgcatt-ttcgtgctagagctttg-------cgcttctttcgcagGGAGAGCTGGAGTCCCCATGGAAGTCATGGGACTGATGCTTGGGGACTTTGTGGACGAGTACACTGTTCGCGTGGTGGACGTCTTTGCGATGCCTCAGAG

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|192296152|gb|FG989032.1|FG989032
EST:     CCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCGAACAC                         GGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTC
genomic: CCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACggtatgctat ... tttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTC
EST: gi|19053660|gb|BM732327.1|BM732327
EST:     CCGAGCATGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACAC                         GGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTC
genomic: CCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACggtatgctat ... tttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTC
EST: gi|213617970|gb|DB957395.1|DB957395
EST:     CCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACAC                         GGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTC
genomic: CCGAGCAGGTCTACATCTCCTCCCTCGCCCTTCTCAAAATGCTCAAACACggtatgctat ... tttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccatgttttttttattgttcatcttataattttgaaaaccctaatttgtgtgtaGGAAGAGCTGGAGTACCGATGGAAGTGATGGGTCTGATGTTGGGGGAGTTCGTGGATGAGTACACCGTTCGCGTTGTGGATGTGTTTGCGATGCCTCAGA
                                       ccctaat  putative branch site (score: 3)
      ttttttttattgttca  TA-rich tract