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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa...

Basic information

species Glycine max
transcript GLYMA09G42180.1
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os10g34710.1 (Oryza sativa), 5'ss of exon 19
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttct---tatatccccag-aatcagaatatttgattatttccatgtactttttaaactaagaaa
 || || ||||||||||| |||||||||||||| |||||||| |||||||||||||||||||||||||| ||||||||||| || || ||||| || ||||| |   | |     ||| ||  | || |  ||    |  |  |   | |||  |||  ||         ||| || | |  |||  | ||  |   |      
AGACCCACTTAGTGTTTCGGTTGCAATTCTTCACCAGTTTAACATTTTGCCTGAGATGTATCAAGTTGGGTACACAAAATTGTTCTTTCGAACTGGCCAGgtgagctaagcagcctttgttttatttattcacttcctggtaatgagtgtattgccaataactgttggccttgtttttctgaatgagcgttaaatgtttg----

upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G113202_T01 (Zea mays), 5'ss of exon 19
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaa----tgaatgtgaatttttttga----agttttatacaatttt----tttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa-------------------------------------------------------------------------------
 ||||| || ||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||| || || |||||||| || ||||| |    ||  | |  | |||  ||      ||   ||   |   |     |  || | ||   | |     |        | |||    || | ||||||   | | |                                                                                 
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGTCAGgttagttctgtttattcagtttcctggcaatggtcacattagaaactgaagctatttgtttcattacatgtttatagaccattcattgttctggattttttaccattatatgtatgcacgaccttttttatttgttaagcatttggtgaaagtgatcttgtgttactgtgtcctttgatattgggctgaag

upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G139583_T02 (Zea mays), 5'ss of exon 19
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaa--tgaatgtg---aatttt---------------tttgaagttttatacaatttttttcttatatccccagaa-----tcagaatatttgattatt-tccatgtactttttaaactaagaaa-----------------------------------------------------------------
 ||||| || ||||||||||||||||||||||||||||| || ||||| ||||||||||||||||||||||||||||| || || |||||||| || ||||| |  |  || |    ||||||               || |||  |  ||  | |  |||  ||| ||    | |      |||   | || |||| || || || || | | |  ||||    |                                                                 
AGATCCACTCAGTGTTTCAGTTGCAATTCTTCATCAGTTCAACATTTTACCTGAGATGTATCAAGTTGGCTACACAAAGTTGTTCTTCCGAACTGGACAGgttagttctatttattcaattttctgccaatggccacattagaaactaaatctattgctttcattacatgtttatagaccattcattgtcttggatttttatctatata-tgtatgtactattttatttttgttttaagcatttggtgaaactaatcttgtgttactttgtccttcgatattgggctgaag

upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 5'ss of exon 23
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa
                    |||| ||||| |||||||||||||| ||||| |||||||||||||||||||||||||| || |||||| |||| || ||||||     |   |  || |  |  | | |  |  | |||| | |||||     ||   ||| | ||  || |     ||||| | ||  |          
--------------------TTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAGgta-----taatagcttgtcggctggtgtcaaagacttttattttata-----aggggcagga-ataagagt---ctcatgtgcattgcag---------

upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 5'ss of exon 20
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa
 ||||| || |||||||||||||| ||||| |||||||||||||| ||||| |||||||||||||||||||||||||| || |||||| |||| || ||||||     |   |  || |  |  | | |  |  | |||| | |||||     ||   ||| | ||  || |     ||||| | ||  |          
AGATCCTCTAAGTGTTTCAGTTGCGATTCTCCATCAGTTTAATATCTTGCCGGAGATGTATCAAGTTGGCTACACAAAGTTGTTTTTCAGAACTGGCCAGgta-----taatagcttgtcggctggtgtcaaagacttttattttata-----aggggcagga-ataagagt---ctcatgtgcattgcag---------

upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 5'ss of exon 20
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa-
 ||||| || |||||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||| |||| || |||||| |  ||    | |  | ||| || ||              |||    ||   ||| |||  |||   ||| | |  | |||||  |  || |    | 
AGATCCTCTAAGTGTTTCGGTTGCAATTCTCCATCAGTTTAATATCTTGCCAGAGATGTACCAAGTTGGCTACACAAAATTGTTTTTCAGAACTGGCCAGgtact--ataactagtcgtctgatgtcttga----------ctttaggggccacaaattaga-cattc--ttactgcagtatacttgcttcaccattgcag

upper sequence: GLYMA09G42180.1 (Glycine max), 5'ss of exon 18
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 5'ss of exon 19
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatg-aatgtgaatttt-tttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa
 ||||| |||||||||||||||||||| ||||||||||| |||||| |||||||||||||||||||||||||||||||||| ||||||||||| || ||||| |    | |||| | |  | |||| |   || || |    |  ||    |    || |           |  | |  ||  |  ||  ||||        
AGATCCACTTAGTGTTTCAGTTGCAATCCTTCATCAGTTCAATATTCTGCCTGAGATGTATCAAGTTGGCTACACAAAATTGTTTTTCCGAACGGGACAGgtgagatgaagtgattatcatctgaactcgcattcagtagggtgattgaccctaatgagttgtggctggaaaacaatgtcactttgttaataaatgctct--

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|26056190|gb|CA799104.1|CA799104
EST:     CTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAG                         ATTGGTGTGCTTGAAGATACTAGAAATCGTACCCTCCATGGCATTTTACGT
genomic: CTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatg ... ggaattgcagATTGGTGTGCTTGAAGATACTAGAAATCGTACCCTCCATGGCATTTTACGT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCCGCTTAGTGTTTCAGTTGCAATTCTTCATCAGTTTAATATTTTGCCTGAGATGTATCAAGTTGGCTACACAAAATTATTTTTCCGAACAGGGCAGgtaatgaatgtgaatttttttgaagttttatacaatttttttcttatatccccagaatcagaatatttgattatttccatgtactttttaaactaagaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG