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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttctataaacattttaaatttttacactctggtaataccatattttaattgcatgtaggattagttgggcatttgtttgagttt...

Basic information

species Glycine max
transcript GLYMA05G03970.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G03970.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 5'ss of exon 15
AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttctataaacattttaaatttttacactctggtaataccatattttaattgcatgtaggattagttgggcatttgtttgagttt--
|  | |||| ||  | || || |  || || ||||| ||||||||||| ||||| || |||||||| ||||||||||||||  | || ||||| |||||||||  | || |||  ||              |   ||  |  || | |   |  || |    |  |   | |  |  ||   | ||  ||| |||||  
AAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAGgttagtagt-tacattccctgccttgtccgcctgtcaatatgcaatgatcactgccaatatgtgatctaccaatgcctgcttattc-ttcattttagtttgg

upper sequence: GLYMA05G03970.1 (Glycine max), 5'ss of exon 14
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 5'ss of exon 9
AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttctataaacattttaaatttttacactctggtaataccatattttaattgcatgtaggattagttgggcat-ttgtttgagttt----
|  | | || || || || |  || || || ||||| ||||||||||| |||||||| ||||| || |||||||| ||||| || || ||||| |||||| ||| |||   || | | |  |  ||  ||| ||    ||| |   | ||   |  ||     | ||    | ||   ||  ||| || ||  |   |    
AACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAGgttggttatatt--ttctttgtttagcttaaaaaattccctactttttcactattttccttctcaagaatt---gtttgtctgctcatgttattccaaaatggtg

upper sequence: GLYMA05G03970.1 (Glycine max), 5'ss of exon 14
lower sequence: GRMZM2G012942_T01 (Zea mays), 5'ss of exon 13
AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttct--ataaacattttaaatttttacactctggtaat-accatattttaattgcatgtaggat-tagttgggca--tttgtttgagttt
|  | |||| ||  | || || | | | || || || ||||||||||| ||||||||||||||||| ||||||||||||||| |||| ||||| |||||||||  | | | ||| |   | |  ||| |  ||  |  |||  ||   ||  || ||||||    |   |||   || || ||  | |  ||||| |      
ATCTGGTGGAGAGTTATCTACCAAGCAGTTGCAGAAAATGGTTCAAGCTCTTCCACAATACAGTGATCAAATTGACAAGCTCACCCTTCATGTTGAGgttagtagttttgttttacatgacatgcatctgcaaactcaacaaactaacaaagacaatatttcttataactgttctatctacttcagtagatttgtct------

upper sequence: GLYMA05G03970.1 (Glycine max), 5'ss of exon 14
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 5'ss of exon 13
AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttctataaacattttaaatttttacactctggtaataccatattttaattgcatgtaggattagttgggcat-ttgtttgagttt-
|| | | | |||  | || ||||| || || || ||||||||||||||| | ||||| |||||||||||||||||||||||||| ||||| |||||||| ||||| |||  | | | ||   |   ||   ||||     |  |   |  |   | || || |    ||||   || |      |  | | | | | | 
AGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAGgt-agttccatacttgtacaattctctccttttcttttcttgttgcgtccac-ctccacttcaacttttggtagtgctactcacaattactctattaatatg

upper sequence: GLYMA05G03970.1 (Glycine max), 5'ss of exon 14
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 5'ss of exon 13
AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttctataaacattttaaatttttacactctggtaataccata-ttttaattgca--tgtaggattagttgggcatttgtttgagttt
|||| |||||||| |||| ||||||||||| |||||||||||||||||  | |||||||| ||||| |||||||| ||||| ||||||||||| ||||||||||   |   |||| ||  | |||  ||  ||   |       ||  |   | | || || || ||   ||  || | |    ||     |||  ||  
AGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAGgttagtttctttttttttttactagcatcgtattttccaaattaaatgtgttgaaacagttctagtttcaatcgtttgacttggcatgc-cacattttggt--

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|19347362|gb|BM892242.1|BM892242
EST:     TCTCCCTCCATGTAGAG                         ATTGCAGGAAAAATTAACAGAATCATTAGGGAGTCAGGACTTCGGGAACTT
genomic: TCTCCCTCCATGTAGAGgttagttcta ... ctttgtccagATTGCAGGAAAAATTAACAGAATCATTAGGGAGTCAGGACTTCGGGAACTT
EST: gi|10844672|gb|BF067898.1|BF067898
EST:     CACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG                         ATTGCAGGAAAAATTAACAGAATCATTAGGGAGTCAGGACTTCGGGAACTT
genomic: CACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttcta ... ctttgtccagATTGCAGGAAAAATTAACAGAATCATTAGGGAGTCAGGACTTCGGGAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTAGTGGTGAAATGTCGACAAGGGACTTACAAAAGATGGTTCAAGCACTTCCACAATACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAGgttagttctatagattttctataaacattttaaatttttacactctggtaataccatattttaattgcatgtaggattagttgggcatttgtttgagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT