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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaatttcttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA

Basic information

species Glycine max
transcript GLYMA09G38110.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------gtataaaatttcttctggggaggtatga-----atatgtatgtttatctt-tgccttttttaata-tatccccca-----taattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                 ||  |   | | || |  | | | |||      | |  ||| ||| |||| ||    | |||||| | ||  ||      || | |||||||||| || || || ||||| ||||||||||| || |||||||| || ||||||||||| ||||||||||||||||| || |||||| |||| |||||
gtaagtttttgctcaattcaggtgcactgctatggaaattcatagttaagtgcatgttcttttatcagtacggatggtggctaaacttatatttctcttctgataatattaataatgtcttccgatgtttattccagGAAGTTCAATTAATCCCAGTGAAAGAACCTATCCAGAAGAGATGATCCAAACAGGGATATCAACCATTGATGTCATGAACTCCATTGCTCGAGGCCAAAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094497_T02 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------------gtataaaatttcttc-tggggaggtatgaatatgtatgtttatctttgcctttt-ttaatatatccccca----taattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                                        || | | |  | ||  |     |   | |||   |  ||  ||||||   |||| | ||||| | | |      |  | |||||||||| || ||||| ||||||||||||||||| ||||||||||| || || |||||||| |||||||||||||||||||| |||||| | || |||||
gtaagtaatttctggttctagcatgctgctctacaatactcatggttaagtgcatgctgtcgtgcagagtaggttttagacgtattggttaattgagttaaatcaatgagtccatctttaaattttgtaaatatgtactctgattttgctgcagGAAGTTCTATTAACCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTCATGAATTCCATTGCTCGTGGACAAAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 6
---------------------------------------------------------------------------gtataaa-atttcttctggggaggtat-gaatatgtatgtttatctttgccttttttaat-atatccccca----taattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                                                            || ||  |||  ||     | || ||  |||   |  ||  ||||||    ||| |||| || | | |      |  | |||||||||| || || || ||||||||||||||||| ||||||||||| || || |||||||| ||||||||||| ||||| || |||||| | || |||||
gtaagtaatttctggttcaagcacgctgctctacaatgctcatggtgaagtgcatgttgtggagagtagtaggttttagaagtattgattgattagcggcattaaatcaatgagtccatctttaaagtttgtaatcatgtactctgattttgttgcagGAAGTTCTATTAATCCCAGTGAGAGAACCTATCCAGAGGAGATGATCCAAACTGGGATATCCACCATTGATGTGATGAACTCCATTGCTCGTGGGCAAAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G38510.5 (Arabidopsis thaliana), 3'ss of exon 7
-------gtataaaatttcttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
       |  | |   |  |       |  ||  |     ||     |        | |  |  || |       |  | |||||||||| ||||| || |||||||||||||||||||| |||||||| ||||| || ||||| ||||||||||||||||| ||||| || ||||| || ||
gtgagctgctttagcctcttgtcacataattactatctcataataaaacacacagatataattctagacttttgtttctccagGAAGTTCTATCAATCCCAGTGAGAGAACCTATCCTGAAGAGATGATTCAGACGGGTATATCCACCATTGATGTCATGAACTCTATCGCCAGAGGACAGAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------gtataaaatttcttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                || |||  ||  ||  | |  |  || | |  |    |  |    ||| |  |  | |     || |  |||||| ||||||||||| |||||||||||||| |||||||| |||||||| ||||||||||| ||||| ||||||||||||||||||||||| ||||| || ||
gtgagttttttaggaggtggtattatttaaccattaaaactcacctctgaactttagagtttacaacagtggcagatcctgtactctttttctttccttttttcagGGAGTTCCATCAATCCTAGTGAGAGAACATATCCTGAAGAGATGATCCAGACAGGGATTTCTACAATTGATGTCATGAATTCTATTGCCAGAGGACAGAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S100_117V6.1 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------gtataaaatttcttctggggaggtatgaa-tatgtatgtttatctttgccttttttaatatatcccccataa-ttcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                           |  |||||||    |||     | ||   |||| ||   ||| || |  ||    | | ||       |   ||||||   ||| ||||||||||||||| | || || |||||||||||||| || || || ||||||||||||||||||||||| ||||||||| ||||||||||
gtgcttgcactcgctttggtacaccttataatcggtaactggctgcaaaattt----tggaatattttgtgctatgaattgctatattcg--ttaaacagtctacttgatgtggcttcagGTGCTTCAATCAACCCTAGTGAGCGGACATACCCTGAGGAGATGATTCAAACTGGAATATCTACCATTGATGTCATGAACTCTATTGCTCGAGGTCAAAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------gtataaaattt--cttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataat-tcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                         |  ||  |   | ||| || |  | |    | |  ||   |  |||||  || ||| |  ||    ||| |  |||||   ||| ||||| || |||||  | || ||||||||||||||||| |||||||| |||||||| |||||||||||||| || || |||||||| |||||
gtgcggtcttttgcttgtcttttccactaacctcagcatcttggaatattttttaaagattgaagagatttgc--ttattagtcaatttgacatgacctcagGTGCTTCGATCAATCCAAGTGAACGGACGTATCCTGAGGAGATGATTCAGACAGGAATATCTACGATTGATGTCATGAACTCCATCGCTAGAGGACAAAA

upper sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------gtataaaatttcttctggggaggtatgaatatgtatgtttatctttgccttttttaatatatcccccataatt-cagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                                  ||        ||  |||     |  ||| || |     ||  | ||  |||  || ||||| |    | ||  ||||    || ||||| ||||||||| | || || || ||||||||||| || ||||| |||||||| |||||||||||||| ||||||||| |||| |||||
gtacttccccttacactacccacattctactcattagccgcaggctcttggaaccttcggaaaattttgaagtaaatatg--tttaatattatattcgatctgatcacagGTGCATCGATCAATCCTAGTGAGCGGACGTACCCAGAGGAGATGATTCAAACAGGAATATCTACGATTGATGTCATGAACTCTATTGCTCGAGGGCAAAA

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|209723248|gb|BW675195.1|BW675195
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|22931741|gb|BU548880.1|BU548880
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|298183011|gb|HO028274.1|HO028274
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|14259630|gb|BG882538.1|BG882538
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|213617416|gb|DB965231.1|DB965231
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|6567285|gb|AW234896.1|AW234896
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAT                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|5342420|gb|AI794704.1|AI794704
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|213607123|gb|DB967000.1|DB967000
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|7589581|gb|AW705352.1|AW705352
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|213592755|gb|DB957813.1|DB957813
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
EST: gi|213602215|gb|DB958475.1|DB958475
EST:     AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAG                         GAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA
genomic: AATTGATAATGGTCCACCCATATTACCCGAGGCTTACTTGGACATATCAGgtataaaatt ... cataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtatgaatatgtatgtttatctttgccttttttaatatatcccccataattcagGAAGTTCCATCAACCCTAGTGAGAGAACCTATCCTGAGGAGATGATACAGACAGGGATATCTACCATTGATGTCATGAATTCTATTGCTAGAGGTCAAAA
                              ttttaat  putative branch site (score: 3)
                                      tatccccc  CT-rich tract
                            ttttttaatatat  TA-rich tract