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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCGGGATCCTCTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctcttaatgtagatttttaggctactaggctttcaccttatcagttattataattataactgcgtaaccctttctttcgaacttttggcag

Basic information

species Glycine max
transcript GLYMA10G27810.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G27810.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
GCAGCGGGATCCTCTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctcttaatgtagatttttaggctactaggctttcaccttatcagttattataattataactgcgtaaccctttctttcgaacttttggcag------
 || || |||||||||||||| ||||| || || || ||||| |||||||||||||||||||| |||||  || | ||||| || || ||||| ||||||||| |    |  | |     |  |   | |  ||   |  |  | |   |    | ||| |    |||  |   |      ||  |    ||          
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctctga--ctcaaacttgcccggtcctttcagtgtttctctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac

upper sequence: GLYMA10G27810.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM5G895400_T01 (Zea mays), 5'ss of exon 1
GCAGCGGGATCCTCTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgt---ttgctcttaatgt-----agatttttaggctactaggctttcaccttatcagttattataatta-taactgcgtaaccctttctttcgaacttttggcag
 || || ||||| |||||||||||||| ||||| || ||||| |||||||| || |||||||| ||||| || || ||||| || |||||||| ||||||||   ||  ||   ||||     | |||| |    | ||| | |||    |||     ||||  ||  | ||| |  | |    | |  ||   ||||       
CCAACGAGATCCCCTTATTGAGTATAAACTTGAGGGATATAATCTTTTCTTAGACATGATGGCTCAAATCAGGAGGAATGTTATTTATTCTGTATATCAGgtaagttcatccacatgtcctaaaaatttctttcatgctacgtttttgttttaaataatatttgaaccactaagtttggagtaatgtaattactacttca-----

upper sequence: GLYMA10G27810.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 5'ss of exon 20
GCAGCGGGATCCTCTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctcttaatgtagatttttaggctactaggctttcaccttat---cagttattata-attataactgcgtaaccctttctttcgaactt-ttggcag-------------------
 ||||||||||| ||||||||||| |||||||||||||| || || |||||||| ||||||||||| |||||||||||||| || |||||  | || ||||| |  | ||||   |||  |    | || |     ||||  || |   ||  | | | | | || |    |  ||  || | |||  | ||     |||                    
ACAGCGGGATCCGCTTATTGAGTACAAGCTTGAAGGCTACAATCTATTCTTGGAGATGATGGCACAGATAAGAAGAAATGTTATTTATTCAATATACCAGgtata-tattaaaccagagct---agatattgtatcttcagtttgtgcacacatgtcacacagtacactcac-caattctctatttttatctcacctgcaatgcccttttcctatggcag

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|5510254|gb|AI856638.1|AI856638
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAG                         TTTCAACCTGTGCTGGTAGAGCAAGATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctctt ... cttttggcagTTTCAACCTGTGCTGGTAGAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|207839425|gb|GD811242.1|GD811242
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAG                         TTTCAACCTGTGCTGGTAGAGCAAGATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctctt ... cttttggcagTTTCAACCTGTGCTGGTAGAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|7686650|gb|AW757307.1|AW757307
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAG                         TTTCAACCTGTGCTGGTAGAGCAAGATCATGACTAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctctt ... cttttggcagTTTCAACCTGTGCTGGTAGAGCAAGATCAGGACAAAACAGAGAATCGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCGGGATCCTCTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTGTATCAGgtttgctcttaatgtagatttttaggctactaggctttcaccttatcagttattataattataactgcgtaaccctttctttcgaacttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA