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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGGCAAGAATTTCGTGTATAACGGTAACATCAATGTTGCTGTTGCTGTGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggcttgactatcctgaagcaatattatggtgattcatgtctaattttctgtgccatactccaactatttgatctatctttatctgagtccaatggtatcttgcgagcaatccatgtagctgacctctcctgattgttgtttttgtctaatttgttatttgattgggtacttgtttcttgttgtgacag

Basic information

species Glycine max
transcript GLYMA20G24830.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24830.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G058702_T01 (Zea mays), 5'ss of exon 2
AGACGGCAAGAATTTCGTGTATAACGGTAACATCAATGTTGCTGTTGCTGTGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggcttgactatcctgaagcaatattatggtgattcatgtctaattttctgtgccatactccaactatttgatctatctttatctgagtccaatggtatcttgcgagcaatccatgtagctgacctctcctgattgttgtttttgtctaatttgttatttgattgggtacttgtttcttgttgtgacag
 || || ||||  |||   || ||| ||||||||||  |||| || |||||||||||| |||||||  | || || ||||||||||||||||| || |||||  ||      || ||| |   |  |||        ||||   |  ||||  | ||   |    | ||| | || ||| | |    |    ||  |||| ||   ||                                                                                      
GGATGGAAAGAGCTTCACATACAACAGTAACATCAACATTGCAGTGGCTGTGGCAATTGATGGTGGCCTTATTACACCTGTTCTTCAGGATGCTGACAAGgtacgt------acaatcttt--gtgata-------aattcggcttcaattcgcagttttag---caaacaagttcatcaaacagctt----gttgaatgttacactgtag-----------------------------------------------------------------------------------

upper sequence: GLYMA20G24830.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 5'ss of exon 2
AGACGGCAAGAATTTCGTGTATAACGGTAACATCAATGTTGCTGTTGCTGTGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggcttgactatcctgaagcaatattatggtgattcatgtctaattttctgtgccatactccaactatttgatctatctttatctgagtccaatggtatcttgcgagcaatccatgtagctgacctctcctgattgttgtttttgtctaatttgttatttgattgggtacttgtttcttgttgtgacag
||| || |||| |||    |||||| | |  || ||  |||| || || |||||||| |||||||| ||||| |||||||||||||||||||| |||||||| | || | ||  | | |||           |||  |||| ||   || ||  |||  | |  || |  ||  |||   || |||   ||| |   |    || | |  |  | |  | ||   | |  | |  |   || |||                                                 
AGATGGGAAGACTTTTACATATAACAGCAGTATAAACATTGCGGTAGCAGTGGCAATCAATGGTGGGTTGATAACCCCTGTTCTTCAGGATGCTGATAAGgtaaatgacatgcattttctg-----------tggaaattcgtgaaaaaattcttgtatcctg-tcaagtta--tgaatgatgttt---tgattttta----atttcgaaattagttta-gttaataatttgtttttgatggtgtag-----------------------------------------------
















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|7926430|gb|AW832456.1|AW832456
EST:     GGCAATTAATGGGTGGTT-GATCACCCCTGTTCTTCAGGATGCNGATTAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
genomic: GGCAATTAATGG-TGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
EST: gi|27809157|gb|CB063579.1|CB063579
EST:     TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
genomic: TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
EST: gi|6069883|gb|AW099479.1|AW099479
EST:     TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCACGATGCGGATAAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAG
genomic: TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAG
EST: gi|193489031|gb|FK456728.1|FK456728
EST:     TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
genomic: TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
EST: gi|193558726|gb|FK512927.1|FK512927
EST:     TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
genomic: TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
EST: gi|193458208|gb|FK422499.1|FK422499
EST:     TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
genomic: TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAAAAAGCT
EST: gi|8283121|gb|BE020682.1|BE020682
EST:     TGGCAATTAATGGTGGGTTGATCACCCCTGTTCTTCAGGATGCGGATAAG                         TTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAA
genomic: TGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggct ... gttgtgacagTTGGACTTGTATCTATTGTCCCAAAAATGGAAGGAGCTAGTGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGGCAAGAATTTCGTGTATAACGGTAACATCAATGTTGCTGTTGCTGTGGCAATTAATGGTGGTTTGATCACCCCTGTTCTTCAGGATGCGGATAAGgtcagtggcttgactatcctgaagcaatattatggtgattcatgtctaattttctgtgccatactccaactatttgatctatctttatctgagtccaatggtatcttgcgagcaatccatgtagctgacctctcctgattgttgtttttgtctaatttgttatttgattgggtacttgtttcttgttgtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG