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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT

Basic information

species Glycine max
transcript GLYMA16G00400.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
              |||||  | | |||    |  |    ||  |  ||   || |  ||| | |  ||||| ||  |  |   | |||| ||||||||||| |||||||||||||||||||| |||||||| |||||||| ||||| || ||||| |||| |||||| |||||||| || |||||||
-------------gtaagt--tttattgac--acagcttttaacgaattcattcttggagtatga--catgttctcgttctctgt-agGTAAAAGGAGAACCCAATGTTTCTTACATCTGTTCTAGATACTATCGTGCTCCAGAACTCATTTTTGGTGCCAGTGAATACACAACTGCAATTGATATAT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G57870.3 (Arabidopsis thaliana), 3'ss of exon 8
gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatg-tgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
      ||  | | ||   ||| |     ||| |||    || | ||  | ||||  | | ||     |||  |  ||    ||  ||||||||||||||||| ||| |||||||||| |||||||||||||| ||||| || || || || ||||| ||||| || || |||||||| ||||| ||||
-----gtaaag-tttatcagctatagctcttagtgg--tttagttttcctagtcc--atgcttagattatgacgtgtcatggtccacagGTGAAAGGAGAACCCAATATTTCTTACATTTGTTCAAGATACTATCGTGCCCCAGAGCTCATTTTTGGAGCCACCGAGTACACAACTGCAATAGACATAT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 6
gtaagatattgatctaagtgctctgttggttaatgg-------aagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
|||| || || ||| |   || ||| |  |||||||       |||  |   | |||  |       | |    ||  |  |||   || ||||||| ||||||||||| ||||||||||| ||||| |||||||| |||||||| || ||||| |||||||| |||||||||||||| ||||| |||||||| |
gtaa-attttcatcca---gcactggttattaatggtgtcatgaagtcatcttgtttcattgcttgatgttggtcagct--ttccgttttatcagGTAAAAGGAGAACCCAATGTTTCTTATATCTGCTCAAGATATTACCGTGCCCCAGAACTCATATTTGGTGCCACTGAATATACGACTGCTATAGATATTT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
                 ||||  | | |    ||   | | ||  | | | ||||   ||  | |     |   | |  | ||  |     ||  ||   ||||||||||| || || ||| | || ||||| |||||  | ||||||||||||||||| ||||| ||||| || || || || || ||||||||||||||||
ctgacgagttgttcgagaagacttcgtttctggtatgcggatgtctca-gtaagcgggtgcgtgtgaa--tagtgatgtaaccgagacgggcttgttgtgcagGTGAAAGGGGAGCCCAATATCTCGTACATTTGTTCGCGGTACTACCGTGCTCCGGAGCTTATTTTTGGAGCGACGGAGTACACGACTGCCATAGATATAT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtaagatattgatctaagtgctctg-ttggttaatggaagctactgttttttgtcctcaagtttcatccat------gtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
        ||   ||| ||  | |       |||  |  ||     | | |||   ||       |   |||  ||      | | ||  | ||   ||||||||||| || |||||| |||| ||||| |||||| |||| ||||||||||| || || |||||||| || || ||||| |||||||| || || ||||
gagtctgcagtggttgctcataatatggaaattgtctcgtgcggtattcagttgaatgcgtgggtgcagcattgatcatagtgagatttgagttgtgcagGTGAAAGGGGAGCCTAATATTTCGTACATTTGTTCACGATATTACCGTGCTCCCGAGCTGATATTTGGAGCTACAGAATACACAACTGCGATTGACATAT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------gtaagatattgatctaagtg--ctctgttggt-taatggaa--gctactgttttttgtcctcaagtttcatccatgtgcttctaattcat---------------cagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
                                               || |   ||  |    | ||  || |  | || |  ||||   | | |  |  ||  |  | | | | | ||   |||   | |  | |                ||||||||||| || || ||| |||| ||||| |||||| | |||||||||||||| || || || ||||| || || || || || |||||||| |||||||
gtgagtatctgttggatgagagtgagcattgttcaaattgtgaggctgtgaaccatccagtggaatggactttacttgtgtggtggagatgttgcactaattcctgattagggtacttctcggtggagcgacatgacggaggtggtgttgtgcagGTGAAAGGGGAGCCCAATATTTCGTACATTTGTTCACGGTACTACCGTGCTCCTGAGCTGATTTTTGGAGCGACAGAGTACACGACTGCCATCGATATAT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gtaagatattgatctaa--gtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcat---cagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
        |||| | || |    ||   ||   | |  | || | ||    | | |||         ||||  |  |  || |  |   | |  |   ||||||||||| ||||||||  | || || ||||||||| | || ||||||||||| || || |||||||| || || ||||| || ||||| ||||| ||||
agtagtgggtaacacatggcatgaataatgtcttctccgcta-tcgagttgaatatttgagtggagaaagtggcgacactgagaattcgagtactgtgcagGTGAAAGGGGAACCTAACATCTCGTATATCTGTTCACGGTATTACCGTGCTCCTGAGCTGATATTTGGAGCGACGGAATACACCACTGCGATAGACATAT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 7
gtaagatattgatctaagtgctctgttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
||  | |  | |   |   | ||  ||||  |||  | ||  ||| |||  ||   |   |||  |            ||   | |||||||||||||| || ||  | || || ||||||||  | || |||||||||||||||||||||||||| || ||||| || ||||| ||||| || || |
gtggg-tgcttacaaataggatcc-ttgg--aattca-gcagctgatttgcgtttcctgcttttcttggca-------aaacaaacagGTGAAAGGAGAGCCCAACATATCGTATATCTGTTCCCGTTATTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

upper sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 7
gtaagatattgatctaagtgctct---gttggttaatggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
              |  |||||      | || |  | | |  | | |    |  |  |   ||||| | | | | ||   ||  || |||||||| ||||| || ||  | || || ||||||||  | ||||||||||||||||||||||||||||| || ||||| || ||||| ||||| || || |
-------------gtgggtgcttacaaataggatccttggaatt-cagcagctgat--ttgcgtttcctgcttttcctggcaaaacaacagGTGAAGGGAGAGCCCAACATATCGTATATCTGTTCCCGTTACTACCGTGCTCCGGAACTTATATTTGGTGCAACTGACTACACAACAGCCATCGACATCT

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|26047783|gb|CA784461.1|CA784461
EST:     CACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTG                         GTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT
genomic: CACACACTCATCAGCTGAAACTATGTGATTTTGGGAGTGCAAAAGTGTTGgtaagatatt ... aattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaagctactgttttttgtcctcaagtttcatccatgtgcttctaattcatcagGTGAAAGGAGAACCTAATGTTTCTTACATCTGTTCAAGATACTACCGTGCTCCGGAACTTATATTTGGGGCCACTGAATATACAACTGCCATAGATATAT
                                         ttctaat  putative branch site (score: 2)
          tgtttttt  TA-rich tract