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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaaattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------gtatttaaattcctttgcagtgttctaca---attgtatgttgatgtgtgagttttttccccc--------taatatcttccca---atatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                          || |||| | | | | |  |  ||   |   || ||   |  |  | |   | | |||            |||| |||||| |    |||| |||||||||| || ||||| ||||| ||||||||||| || |||||||| || ||||| ||||| || |||||||||||||| || |||||| |||| |||||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------gtatttaaattcctttgc--agtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                                       |  |||| |    || |   | ||   || |    |  ||  || | | | |||| |     |  ||   |     |  | |||||||||| || || || ||||||||||||||||| ||||||||||| || || || ||||| || ||||||||||||||||| |||||| | || |||||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatg-tactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------gtatttaaattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                                                  | |  |||  || || |  ||  |  | ||   ||  || | | |  ||| |   | |  ||   |     | || |||||||||| || ||||| ||||||||||||||||| ||||||||||| || || || ||||| || |||||||| ||||| || |||||| | || |||||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatga--gtccatctttaaagtttgtaatcatg-tactctgattttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
-----gtatttaaattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
      |  || |    |||  ||      ||| ||   ||  | |          | |    |   |  | |      |  | |||||||||| |||||||| |||||||||||||||||||| |||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||| || ||
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagactttt----gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------gtatttaaattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                ||| ||| ||   | | |   | || | || ||      || |    |  | | | | |  | |||| ||  | ||||||| |||||||||||||||||||||||||| |||||||| |||||||| |||||||| || ||||||||||||||||||||||||||||| ||||| || ||
gtgagttttttaggaggtggtattatttaaccattaaaactcacct-ctgaactttagagtt-tacaacagtg-gcagatcctgtactctt--tttctttcct-tttttcagGGAGTTCCATCAATCCTAGTGAGAGAACATATCCTGAAGAGATGATCCAGACAGGGATTTCTACAATTGATGTCATGAATTCTATTGCCAGAGGACAGAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------gtatttaa-attcctttgcagtgttctacaattgtatgt-tgatgtgtgagttttttccccctaatatcttcccaatat---ttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                            || |    |      ||||   || |  |||  | |||   |||  |   | | |||     |   ||| |   || |   ||||||   ||| ||||| ||||||||| | || || |||||||||||||| || || ||||||||||| |||||||||||||| ||||||||| ||||||||||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgctatgaattgctatattcgttaaacagtctacttgatgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------gtatttaaattcctttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                   | ||  | |  | |     | ||  |  ||| | |   |||    ||| |||           |  ||  ||  |  |||||   ||| |||||||| |||||  | || ||||||||||||||||| ||||||||||||||||| |||||||||||||| || || |||||||| |||||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgcttattagtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------gtatttaaattcct--ttgcagtgttctacaattgtatgttgatgtgtgagttttttccccctaatatctt-cccaat---atttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                       |||  | |   |    ||||  |  |  ||   |  |   || | |||  |   |     ||||||  |   | ||   ||  ||||    || ||||||||||||||| | || || || ||||||||||| || |||||||||||||| |||||||||||||| ||||||||| |||| |||||
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaat-tttgaagtaaatatgtttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA

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|209701922|gb|BW664576.1|BW664576
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaaat ... aatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|151411391|gb|EV281202.1|EV281202
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaaat ... aatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|23729967|gb|BU763089.1|BU763089
EST:     ATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
genomic: ATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaaat ... aatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|209713872|gb|BW684065.1|BW684065
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaaat ... aatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattgtatgttgatgtgtgagttttttccccctaatatcttcccaatatttcagGAAGTTCCATCAATCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                              ccctaat  putative branch site (score: 3)
                                      tcttccca  CT-rich tract
                                 taatatctt  TA-rich tract