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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA

Basic information

species Glycine max
transcript GLYMA11G19550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 3'ss of exon 4
gtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggc-agCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
||||||  |   |||  |||||||    |  ||||  ||  ||    | |||| |||   |   |  | | ||| | |   | |||||| || || ||||||||| | |||||||||||||| || || || || |||||||||||  ||||||| || ||||||||  |||||||||| |||||
gtgagtgca---gtaacttttgtt---attcatgtcattacctgaacactttg-taaccgtg--tgctttttgagctttaaccagCTGAAGGAGCAGAAAATGGCCTTGAGTTCACAATTGTGAGACCTTTCAATTGGATTGGACCAAGAATGGACTTTATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G167872_T02 (Zea mays), 3'ss of exon 2
gtgagttgatttgtattttttgtt------ttggtgtatgtttttttctttcaattttgata-attcttactagtgtg---tgatcatc-ggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
|| ||| || |   |||||    |       || ||    | || ||||  || || |  ||  || ||   | | ||   |||  ||| | ||||||||||||| ||||||||| | || |||||||| || || || ||||| |||||||| ||  | |||||||||||||||||  | |||||||| |||||
gtcagtagagtaaaattttgcactgtgccgctgatggccttcttgttctaacacttcttttatgtttttgtcattttgatttgagtatctgccagCTGAGGGTGCAGAAAATGGCCTTGAATTCACAATCGTGAGACCTTTTAATTGGATTGGGCCAAGGATGGATTTCATTCCTGGTGTCGATGGTCCTAGTGA

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G063949_T01 (Zea mays), 3'ss of exon 4
----gtgagttgatttgtattttttgttttggtgta--tgtt--tttttctttcaattttgataattcttactagtgtgtgatca-----tcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
    || | ||   ||||  ||||||     |||||  || |  | || |||    |||| || ||| ||   | | | | ||        |  ||||||| ||||| ||||||||| | || |||||||| || || || || || |||||||||||  | ||||| |||||||||||  |||||||||| |||||
gttagtaaattagcttgttatttttgccactgtgtagctgatggtcttccttctcgttttaattattattgtcatttttttattgaacatccaccagCTGAAGGTGCAGAAAATGGCCTTGATTTCACAATCGTGAGACCTTTCAATTGGATTGGACCAAGGATGGACTTCATTCCTGGTGTTGATGGTCCTAGTGA

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
         |  | |||| | ||||  |   |||||  |       ||   |    | |     |    |||       | |||||||||||||||| |||||  | |||||||| || ||| | || |||||||||||||||||| | ||||||||||| || || ||||||||||| || ||
--------gtaagcatttct-gtttaagatgatgttggtaaaaacaaaaggtttacacttaacttcacttgtttcttgtgacagCTGAGGGTGCTGAGAATGGGCTTGAGTTCACCATCGTACGACCTTTTAACTGGATTGGACCTAGGATGGATTTCATCCCCGGCATTGATGGTCCTAGCGA

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagttgatttgtattttttgttt-tggtgtatgtttttttctttcaattttgataa---ttcttac-tagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
         | |||| ||||  |    |    |  ||||||  ||  |      | ||   |||| || |    | |        ||||||||||||||||| |||||  | |||||||| |||||||| ||||| ||||||||||||||| | ||||||||||| ||||| ||||||||||| || ||
--------gtatgtagttttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcagCTGAGGGTGCTGAGAATGGACTCGAGTTCACCATTGTAAGACCATTCAACTGGATTGGACCTAGGATGGATTTCATCCCTGGCATTGATGGTCCTAGCGA

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 3'ss of exon 4
------------gtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
             |   | ||| ||||  |||    || |  |  || | | || | || |  |  | ||| ||| |  | | | ||  |   |||||||||||||||| |||| | | |||||||| ||||| ||||| |||||||||||||| ||  |||||||||| |||||||| ||||||||||| || ||
gtgagtgaacttttccatcgatctgtacgttt---cttagcatgcgtgtgtatcataca-tccttctcatttttattt-tttttcattgtttacagCTGAGGGTGCTGAGAATGACCTAGAGTTCACCATTGTGAGGCCCTTTAACTGGATTGGGCCCAGAATGGATTTTATTCCTGGCATTGATGGTCCTAGCGA

upper sequence: GLYMA11G19550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 3'ss of exon 4
gtgagttgatttgtattttt-------tgttttggtgtatgtttttttctttca-attttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
||||||  | || |   |         |||||      |||  | | |||   | || ||  ||||| ||  |    | | || ||   ||||||| ||||| || |||||| | |||||||| ||||| ||||| |||||||||||||| ||| ||||||||||||||||||| ||||||||||| |||||
gtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacagCTGAAGGTGCAGAGAATGGCCTAGAGTTCACCATTGTGAGGCCTTTTAACTGGATTGGGCCTAGAATGGATTTCATTCCTGGCATTGATGGTCCTAGTGA

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|7478600|gb|AW666329.1|AW666329
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|193692175|gb|FK631970.1|FK631970
EST:     TAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: -AGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|209702421|gb|BW656397.1|BW656397
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCT
EST: gi|193491410|gb|FK456073.1|FK456073
EST:     GGTGGTCTTATGTCTATGTGC-AAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GGTGGTCTTATG-C-ATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|6481482|gb|AW200753.1|AW200753
EST:     GAGGTGGGCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGCGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|193530421|gb|FK486620.1|FK486620
EST:     TAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: -AGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|7283460|gb|AW596067.1|AW596067
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|193557146|gb|FK512789.1|FK512789
EST:     AGGTTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: AGG-TGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|9440275|gb|BE440783.1|BE440783
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|27445843|gb|CA952966.1|CA952966
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|18039430|gb|BM307724.1|BM307724
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|193518856|gb|FK474537.1|FK474537
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         TTGAGGGTGCTGAAAATGGCTTGGAGTTCACA
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACA
EST: gi|193469939|gb|FK437280.1|FK437280
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
EST: gi|14008730|gb|BG725334.1|BG725334
EST:     GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTG                         CTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT
genomic: GAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgat ... tcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcagCTGAGGGTGCTGAAAATGGCTTGGAGTTCACAATTGTAAGGCCATTTAACTGGATTGGACCTCGAATGGATTTCATTCCTGGGATTGATGGTCCAAGTGA
                            ttcttac  putative branch site (score: 2)
     tttttttctttcaatt  TA-rich tract