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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttaacttcctttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatcttcccaatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

Basic information

species Glycine max
transcript GLYMA10G42940.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------gtatttaacttcctttgcagtgttctacaatt-gtatgt-tgatgtgtgaatttttaccccc----------------taatatcttccca---atatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                     ||| |   |    |||| ||||||   ||  ||| |  || ||  | || || ||   |                 |||| |||||| |    |||  |||||||||| || ||||| |||||  ||||||| || || |||||||| || || || ||||| || |||||||||||||| || |||||| |||| |||||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgca-tgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------gtatttaacttcctttgca-gtgttctacaattg---tatgttgatgtgtgaatttttacccccta-----atatcttcccaatatgt--cagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                             ||    |      |||  | || ||    |||||   ||  |  ||| ||  || ||||     |      || |  ||  | | ||   |||||||||| || || || |||||| ||||||| || ||||||||||| || ||||| ||||| || ||||||||||||||||| |||||| | || |||||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------gtatttaacttcctttgcagtgttctacaattg----tatgttgatgtgtgaatttttacccccta-----atatcttcccaatatgt--cagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                                 ||| |    ||     | | || |  |  |  |    ||  |  ||| ||  || ||||     |      || |  ||  | | |||  |||||||||| || ||||| |||||| ||||||| || ||||||||||| || ||||| ||||| || |||||||| ||||| || |||||| | || |||||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgattttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
-----gtatttaacttcctttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatcttcccaatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
      |  || |    |||  ||      ||| ||   ||  | |       |  | ||   |   |  | |      |    |||||||||| |||||||| |||||| ||||||| ||||| |||||||| ||||| || ||||| || |||||||||||||| ||||| || ||||| || ||
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagactttt----gtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 6
----------------------gtatttaacttcctttgcagtgttctacaattgtatgttgat----gtgtgaatttttaccccctaatatcttcccaatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                       ||||||||        |     |||  | ||    ||| |     |||  |  |  |   | ||  |   ||||   | | ||||| ||||||||||||||||||||| |||| || ||||| |||||||| ||||| || || ||||||||||||||||||||||||||||| ||||| || ||
gtgagttttttaggaggtggtattatttaaccattaaaactcacctctgaactttagagtttacaacagtggcagatcctgtactctttttctttcct--tttttcagGGAGTTCCATCAATCCTAGTGAGAGAACATATCCTGAAGAGATGATCCAGACAGGGATTTCTACAATTGATGTCATGAATTCTATTGCCAGAGGACAGAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------gtatttaacttcctttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatcttcccaatatg---tcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                               |   |||||  ||    | | ||  |  ||| | || | |||  |   | | | |     |   ||| |   || ||   |||||   ||| ||||| ||||||||||| || ||||||||||||||||| || |||||||||||||| |||||||||||||| ||||||||| ||||||||||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattttggaatattttgtgct-atgaattgctatattcgttaaacagtctacttgatgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtatttaacttcctttgcagtgttctacaattgtatgttgatgt-gtgaatttttaccccctaat-atcttcccaatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                || |||  |        |||  |  |  |||  | | |  |  | |   |  ||| |    || | |  ||  ||  |  |||||   ||| |||||||| ||||| || || || |||||||||||||| ||||| ||||||||||| |||||||||||||| || || |||||||| |||||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgcttattagtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------gtatttaacttcct--ttgcagtgttctacaattgtatgttgatgtgtgaatttttaccccctaatatctt-cccaatatgtcagGAAGT---TCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                       |||  |||   |    ||||  |  |  ||   |  |   || | |||| |         ||||||  |   | || ||     | ||   || ||||||||||||||||| || ||||| ||||||||||| || || ||||||||||| |||||||||||||| ||||||||| |||| |||||
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|120533616|gb|EH261749.1|EH261749
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
EST: gi|16278890|gb|BI943147.1|BI943147
EST:     AATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
genomic: AATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
EST: gi|120533425|gb|EH261558.1|EH261558
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
EST: gi|19053577|gb|BM732244.1|BM732244
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
EST: gi|213596831|gb|DB964094.1|DB964094
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGA
EST: gi|208145241|gb|GD941760.1|GD941760
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGACATTTCTG                         GAAGTTCCATCAATCCTAGTGAGC
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGC
EST: gi|213615425|gb|DB965511.1|DB965511
EST:     AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTG                         GAAGTTC-ATCAATCCTAGTGAGCGAACCTACC
genomic: AATTGATAATGGTCCACCAATTTTACCTGAGGCTTACCTGGATATTTCTGgtatttaact ... aatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattgtatgttgatgtgtgaatttttaccccctaatatcttcccaatatgtcagGAAGTTCCATCAATCCTAGTGAGCGAACCTACCCTGAGGAGATGATACAGACTGGAATATCTACAATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                              ccctaat  putative branch site (score: 3)
                                      tcttccca  CT-rich tract
                  tgaattttta  TA-rich tract