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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA

Basic information

species Glycine max
transcript GLYMA11G05190.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 4
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctaca-ttttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                          |||       |   ||    |  |      || |  |||    | | || ||  |||||   | | | |     | |     || | |     || | | | ||||| |||||||||||||| || || || ||||| || || ||||||||||| ||||| || || || |||||||| || || || ||||| ||||||||||
-----------------------------------------aatttagttgtcttgagttgtactaccatccatttcatgccctcatagttctatgcactt---tttcactcccaaaattt---ctcactgtgctatctgtttgcagGTGGCAAAAGAAAGTGCTGACGTGATTATTCTTGACGACAACTTCTCCACTATAGTCACTGTTGCTAAATGGGGTCGGTCAGTGTACATTAATATTCAGA

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttc--agGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                              ||   ||| | |   | ||  |  ||    |    || ||   |  ||| | ||     ||| |    |  || ||  | | |  |||| || |  |   |||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || || || || || |||||||| || || |||||||| || |||||||
----------------------------------------------tagatacccatgaccatgagtaacaatcaattacatgatat-ctcgagttatttgctatttactcccattttg-aatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                                          |  |  | | |  ||  || || |    |||||  |  |  |||     |||      ||  ||| |  | |||  |||    || |||| || ||||| || || |||||||| ||||| || |||||||||  |||||| || ||||| || |||||||||||||| ||||||||||| || ||||
----------------------------------------------------------gtgagtatatgataagattttgttatgtcatttgtgagagctaaag---aat------ctaaaagtttctatctgtataaccttttagGTGGCGAAAGAGAGCGCTGATGTCATCATTCTCGACGATAACTTCAGCACGATCGTCACAGTTGCTAAATGGGGACGTTCTGTTTACATAAACATCCAGA

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattt-tgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                                                          ||     |  || ||   | | | |  | | ||| | |    ||  |      |||| || | |    || |||| || ||||| | ||| |||||||| ||||| || |||||||||  ||| || || || || || |||||||||||||| |||||||| || |||||||
--------------------------------------------------------------------------gtgagtatcatatatccaaataagtctaatgttattatgcaaacgactcaaacatttttttaaactcttttagGTAGCGAAAGAGATTGCGGATGTCATCATTCTCGACGATAACTTCAGCACAATCGTCACCGTAGCGAAATGGGGACGTTCTGTTTACATTAACATTCAGA

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                           |   |  ||      || |  |     ||||  |       | || ||    || |        | |     | |  ||   | | |    ||  |  ||||||| || ||||| ||||| ||||| |||||  |||||||||| |||||||| || |  || |||||||||||||||||||| || |||||||||||||| |
-------------------------------------------taaaagtcattgcttgatacaatctacaaattctcattgtttgcacttcctccatt--gtgaacagtaccaaattctaattaattctgcccatgaac-ttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA

upper sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                       |  ||   |  ||      || |  |     ||||  |       | || ||      ||  | | | ||    ||||   |  ||||||         |  ||||||| || ||||| ||||| ||||| |||||  |||||||||| |||||||| || |  || |||||||||||||||||||| || |||||||||||||| |
---------------------------------------taaataaaagtcattgcttgatacaatctacaaattctcattgtttgcacttc-----ctccattgtgaaca--gtaccaaattctaattctgcccatgaacttcagGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA

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|18733946|gb|BM527900.1|BM527900
EST:     CACTTCATGAAGCTGACATTGGACTTGCAATGGGCATTGCTGGAACTGAG                         GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAGgtgagtgcaa ... atatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
EST: gi|105633721|gb|DW247084.1|DW247084
EST:     CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAG                         GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAGgtgagtgcaa ... atatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
EST: gi|17519533|gb|BM188575.1|BM188575
EST:     CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAG                         GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAGgtgagtgcaa ... atatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
EST: gi|17518979|gb|BM188021.1|BM188021
EST:     CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAG                         GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAGgtgagtgcaa ... atatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
EST: gi|13240205|gb|BG359514.1|BG359514
EST:     CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAG                         GTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG
genomic: CCCTTCATGAAGCTGACATTGGACTTGCAATGGGAATTGCTGGAACTGAGgtgagtgcaa ... atatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttcagGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA
                                      tcttaat  putative branch site (score: 3)
                                 taatttcttaatatat  TA-rich tract