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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAACATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttggtggtgatttactggttttatttttttggggaaaatctgttgatgttaatttctgtgaacag

Basic information

species Glycine max
transcript GLYMA09G23250.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G23250.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G058491_T01 (Zea mays), 5'ss of exon 12
AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAAC---ATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttggtggtgatttac-tggttttatttttttggggaaaatc----------------tgttgatgttaatttctgtgaacag------------------------------------------------------------------------------
    ||  ||  |   ||| || | || ||||||    |||||    | |||||||| ||||| |||||||||||||||||||||| |||||| ||||| ||||| | |          ||  |   |     ||        | ||||                      ||| |   |||||| ||| |                                                                               
---CATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAGGGCTGGACTTCAAGGAGCTAGCAACCATGACAGAAGGATATAGTGGAAGTGATCTCAAGgtcagtagcatgaaacatgaatgcgcacacatgcccccatgaaaaacaaaggcaccatgctcaacaccgatttatttttctgagaatacgcaagatagttgtgtatctctgtattaagagctaaagtagagatcaattatgctcgacactgaattcttctttaacag

upper sequence: GLYMA09G23250.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G159307_T01 (Zea mays), 5'ss of exon 12
AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAAC---ATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaat----tttggtggtgatttactggttttatttttttggggaaaatctgttgatgttaatttctgtgaacag--------------------------------------------
    ||  ||  |   ||| || | || ||||||    ||||||   |  ||||||| ||||| |||||||||||||||||||||| |||||| ||||| ||||| | |    |    |   |||||| |  || |     | ||    | | ||||  ||  |  | | || ||||                                              
---CATAATGCGGCGACTTCTGTCAAAGGAGAAAGTTGATGAAAGGCTGAACTTCAAGGAGCTAGCAACCATGACAGAAGGATATAGTGGAAGTGATCTCAAGgtcagtaacatgaactctcgatttattttttctgagaatgtgtaagagagctgtgtatcgttgtat-tgagaactaaagtagagatcaattctgctcgatcctgaattcttctttaacag

upper sequence: GLYMA09G23250.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 5'ss of exon 13
AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAACATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgt--gaattt----tggtggtgatttactggttttatttttttggggaaaatctgttgatgttaatttctgtgaacag
 |||||| |||||||||| |||||||||||  ||   ||  |  | ||||| || ||||| ||||||||||||||||| ||||||||||| |||||||||||  | | ||    |||   ||||  | || ||     |     | |   | || |||   ||||    ||  |||||
GATGATCCTGAAGACTCTCTTGGCTAAAGAACAAGCCGAGGATCTTGACTTTAAGGAGCTTGCAACCATGACAGAAGGTTATACTGGAAGTGATCTTAAGgtttgtacttctgatggcaatgatgaattgattaagaatcagctgtgttga-ctcttgggattaacaattg-aaacag

upper sequence: GLYMA09G23250.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv16s0050g01830.t01 (Vitis vinifera), 5'ss of exon 12
AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAACATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttggtggtgat-ttactggttttatttttttggggaaaatctgttgatgttaatttctgtgaacag------------
 ||||| ||||||||||| ||||| ||||| |||   ||  |  | ||||| || ||||| ||||||||||||||||| ||||||||||| |||||||||||   |  |  |  |||  | | ||||   | ||  ||  | |    |||||| |||| | |  || ||  |             
GATGATATTGAAGACTCTCTTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCAACCATGACAGAAGGTTATACTGGAAGTGATCTTAAGgtttgtacttctactgacatcaatggtg--aattgattaagaatctgctgttg-tgttgactcttgggattaatcgttgaaacag

upper sequence: GLYMA09G23250.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 5'ss of exon 14
AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAACATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttggtggtgatt-tactggttttatttttttggggaaaatctgttgatgttaattt---ctgt--gaacag
 |||||||||||||||||  |||| ||||| |||   ||  |  | ||||| || ||||| ||||||||||||||||||||||||||||| |||||||||||   |  |  |  ||||   | ||||    |  ||  |    |  | ||||||  ||    |   || |   |||||
GATGATCTTGAAGACTCTCCTGGCAAAAGAAAAAGCAGAGGATCTTGACTTTAAGGAGCTTGCAACCATGACAGAAGGATATACTGGAAGTGATCTTAAGgtttgtacttctactgatggcaatggtgaattgattaagaatcagctgtgttgaccttggcattaactattgaaacag

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|6913165|gb|AW394695.1|AW394695
EST:     TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAG                         AATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
genomic: TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttg ... ctgtgaacagAATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
EST: gi|58021184|gb|CX707926.1|CX707926
EST:     TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAG                         AATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
genomic: TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttg ... ctgtgaacagAATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
EST: gi|58021000|gb|CX707742.1|CX707742
EST:     TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAG                         AATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
genomic: TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttg ... ctgtgaacagAATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
EST: gi|58014250|gb|CX700992.1|CX700992
EST:     TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAG                         AATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
genomic: TCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttg ... ctgtgaacagAATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
EST: gi|9439963|gb|BE440475.1|BE440475
EST:     GGAAGCGATCTTAAG                         AATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG
genomic: GGAAGCGATCTTAAGgtgaattttg ... ctgtgaacagAATTTGTGCATCACTGCGGCTTATCGACCTGTTAGAGAACTAATACAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGATCTTGAAGACTCTTTTGGCTAAAGAGAAACATGAAAACTTAGACTTCAAAGAGCTGGCAACCATGACAGAAGGATATACTGGAAGCGATCTTAAGgtgaattttggtggtgatttactggttttatttttttggggaaaatctgttgatgttaatttctgtgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG