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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG

Basic information

species Glycine max
transcript GLYMA09G40150.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g37740.1 (Oryza sativa), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
              |||  |    | |||  |  || ||   |     | ||     |||| |  |  |   ||||   |||   | |  || |    | ||||||| ||||| |||||||| ||||||||||| | ||||||||||||||| ||  | ||||| || || |||||||||||||| || |||||||| |||
--------------gtttctatctcctgtcatccattagagac--agtaatttaggtctgtggact--gatccatt---tcttgtttt--tttttcttattatagATTTTGGGTACACCAACTAGAGAAGAAATCAGGTGCATGAATCCAAACTATTCTGAATTCAAATTCCCTCAGATAAAAGCTCATCCATGGCACAAG

upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G131853_T01 (Zea mays), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
          |||  |    ||||     |  | || |  |   ||   || | |   ||| || |     |  ||   |||         | | | ||    |||| ||||| || ||||| ||||| || || | ||||||||||||||||||  ||||||| ||||| |||||||||||||| || |||||||| |||
--------gtttgcatctgctatcaaatcgtgtcatgaaatcactg---gtggtactttgtaggctgaatgttttttcttct--------ctttcttcatccaagATTTTGGGTACTCCAACAAGAGAGGAGATCAGGTGCATGAATCCAAATTATTCCGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG

upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
                      |     |    ||| |  | |    ||    |      |   || | ||  | ||  | |   |    ||   ||||    |||| ||||| || ||||| ||||| ||||| | ||||||||||||||||||  | ||||| ||||| |||||||||||||| || |||||||| |||
---------------------gtttgcatctgctatcaaatgccatgaaaccactggtgatactttgtagactaatgtttttctttcccttttgatcca----agATTTTGGGTACTCCAACAAGAGAGGAAATCAGGTGCATGAATCCAAATTATTCTGAATTCAAGTTCCCTCAGATAAAAGCCCATCCATGGCACAAG

upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G00720.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
                |  ||| |||  | | |  |   |||| |     |    ||   |   | ||  ||     | | |     |   ||  || ||   ||||  | || || || || ||||||||||||  ||| |||||||| |||||||| || || ||||||||||| || ||||| ||||| ||||| |||
---------------gtacttaacctgatccctcgt---gttcct-----tcatctctcttctatatttaatttactagtttactcatctgtacatctacc--agATTCTTGGGACGCCTACAAGAGAAGAAATACGGTGTATGAATCCGAATTACACAGAGTTCAAGTTTCCTCAAATCAAAGCTCACCCGTGGCACAAG

upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv15s0048g02010.t01 (Vitis vinifera), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaatt--atgtc-cactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
              |||   ||||     |||||     ||| || |   |    || |  |  || | | |||   || | |  |||  ||  ||||       |||||  |||| ||||| |||||||||||||| ||||||||||||||||||||||  || || |||||||| || || ||||| ||||||||||| |||
--------------gtttgctatcaagtggcttttct--gttattcactttcttttcttaata-ttataggtcagctaagcaggatgttgttgcatgttatgtcttagATTCTGGGTACACCCACCAGAGAAGAAATTAAGTGCATGAATCCAAATTACAATGAGTTCAAGTTTCCACAAATCAAAGCTCACCCATGGCACAAG

upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
                           || |   ||    ||||||    ||   | |||||  |||||    | |   |||   |  |    || |   |  || |||| || || || ||  | || ||||| || |||||||||||||| ||||| || |||||||| |||||||| ||||| || || ||||| |||
---------------------------gtacgc-atgca-ttcttgctcttttttttctgttttttttgcg--agtcgctcttgctcaagacttg-cttttgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtaaagtttattgtgttctttatccttgtgctttataaggttcttgaaagttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
                                   || |    |  |   ||||   || ||   |||     | |   |||   |  |    || |   |  || |||| || || || ||  | || ||||| || |||||||||||||| ||||| || |||||||| |||||||| ||||| || || ||||| |||
----------------------------------gtacg--catgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttg-cttttgcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

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|18734580|gb|BM528264.1|BM528264
EST:     GAGATCATTAAG                         ATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTAC
genomic: GAGATCATTAAGgtaaagttta ... tccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTAC
EST: gi|15337648|gb|BI498304.1|BI498304
EST:     CAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAG                         ATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTAC
genomic: CAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGgtaaagttta ... tccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTAC
EST: gi|209727344|gb|BW655275.1|BW655275
EST:     CAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAG                         ATC-TGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTAC
genomic: CAATGTTTCCCGGAGAGAGTGGGGTTGATCAATTGGTAGAGATCATTAAGgtaaagttta ... tccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatcctgttggttttggatcattgaatctgagtgtaattatgtccactatagATCTTGGGAACACCAACCAGAGAAGAAATAAAGTGCATGAATCCAAATTACACCGAATTTAAGTTTCCTCAGATAAAAGCACACCCATGGCATAAG
                                   tgtaattat  TA-rich tract