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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag

Basic information

species Glycine max
transcript GLYMA11G19550.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g73790.1 (Oryza sativa), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag-
|| || |||||||| ||||| || |||||||||||| | || | ||| ||| | ||||||||||||||||| || ||| | ||||||||||| |||||||||||||  |   |||  |||||||    |  ||||  ||  ||    | |||| |||   |   |  | | ||| | |   |   
GTACTGAAAGAAGATGAATCCCCCTGCATTTTTGGTCCAATTGTGAAACAGCGATGGTCTTATGCATGTGCGAAGCAGCTTATTGAGAGGCTTATTTTTGgtgagtgca---gtaacttttgtt---attcatgtcattacctgaacactttg-taaccgtg--tgctttttgagctttaaccag

upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G27860.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgtt-ttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag
||||||||||||||    || |||||||| |||||||| || ||||||||||||||||| ||||| |||||||| ||  |||||||||| ||  |||  ||| ||    | ||| |    || | |||||  |          || || ||      |   | ||| || | |  | |  |    
GTTCTTAAAGAAGATATTTCCCCTTGCATATTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCGTGTGCAAAGCAACTGATTGAGAGACTTGTTTACGgtaagcatttctgtttaagatgatgttggtaaaaacaaaaggtttacactt------aacttcacttgtttcttgtgacag----

upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag---
|| || ||||||||   ||| |||||||| |||||||| || ||||||||||||||||| ||||| |||||||| ||  | |||||||| ||  |||  |||  || |       ||| ||        | |  ||||| | | |  |     | || | |  |  ||   |  |    ||  |   
GTACTCAAAGAAGATATATCCCCTTGCATCTTTGGTTCAATTGAGAAGCAGAGGTGGTCATATGCTTGTGCAAAGCAACTTATTGAGAGACTTGTTTACGgtatgtagt------tttcttacacgaaagaaattttttgtttctagacacaaaaaagtttctcacgtcacttttttctggttgcag

upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgt------attttt---tgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag
|| || |||||||| |  || || |||||||||||| | || ||||||||||||||||| ||||| |||||||| || |||||||||||| |||||| ||||||||  | || |      || | |   | | || |  |  || | | || | || |  |  | ||| ||| |  | | | ||  |   |||
GTCCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTCCGATTGAGAAGCAGAGGTGGTCCTATGCCTGTGCAAAGCAATTGATTGAGAGGTTGATTTATGgtgagtgaacttttccatcgatctgtacgtttcttagcatgcgtgtgtatcataca-tccttctcatttttattt-tttttcattgtttacag

upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttt-------tgttttggtgtatgtttttttctttca-attttgataattcttactagtgtgtgatcatcggcag
 |||| |||||||| |  || || |||||||||||||| || ||||||||||| ||||| ||||| |||||||| || || ||||||||| |||||| ||||||||  | || |   |         |||||      |||  | | |||   | || ||  ||||| ||  |    | | || ||   |||
CTTCTCAAAGAAGATGCCTCCCCCTGCATTTTTGGTTCAATTGAGAAGCAGAGATGGTCCTATGCCTGTGCAAAGCAATTAATTGAGAGGTTGATTTATGgtgagtcaacttttccatcaatctggatgtttcttaacatgcatctgtctcatagatctttctaattttttttttattattattatttacag

upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ18978 (Selaginella moellendorffii), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag
|| ||||| || ||||| |||||||||||||||||  | || ||||||||| | ||||| ||||| |||||||| ||| |||| ||| |  | || | |||| ||   | ||    | ||||        || ||  | |  ||    | ||    | |||| | ||                 
GTGCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCGAGCGTGTCATCTATGgtaagcaaagttt--ctgtttgaaagaaactaagtcatgtggttgtggtgttatataatctttccag-----------------

upper sequence: GLYMA11G19550.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ07025 (Selaginella moellendorffii), 5'ss of exon 4
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaat-tttgataattcttactagtgtgtgatcatcggcag
|| ||||| || ||||| |||||||||||||||||  | || ||||||||| | ||||| ||||| |||||||| ||| |||| ||| |  | || | |||| ||   | ||    | ||||        || ||| | |  ||    | ||| ||||| ||| | ||                 
GTCCTTAAGGAGGACGAGTCTCCTTGCATTTTTGGCCCGATTGAGAAGCAGCGATGGTCGTATGCTTGTGCAAAGCAGCTGATCGAGCGTGTCATCTATGgtaagcaaagttt--ctgtttgaaagaaactaagttatgtggttgtggtgttttataat-ctttccag-----------------

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

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTAAAGAAGACGAATCTCCTTGCATTTTTGGTTCTATCGAGAAGCAGAGGTGGTCTTATGCATGTGCAAAACAGTTGATTGAGAGGCTGATTTTTGgtgagttgatttgtattttttgttttggtgtatgtttttttctttcaattttgataattcttactagtgtgtgatcatcggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT