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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatgattatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC

Basic information

species Glycine max
transcript GLYMA18G26190.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
gtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatga-ttatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC
|||   ||||| ||   |  |   |  ||  || ||     | |||||     |||||||| ||   |    |  ||  ||    ||||   ||||||||| ||||||||||| ||||| || |  ||||| |||||||| ||||| ||||| ||||| ||||| ||||||||| |||| ||||| || ||| | |
gtaatttctttggcaatttgctcca--tgattcttcaactgtcttgcta----tttaatgagttggatgactaagtt--tgtctgtttgt--acagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 3
gtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatgattatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC
|||   || | ||       |||   |||  ||||    | | || |  | | || |    ||| |   || |  ||     ||||| |   |||||||| ||||||||||||||||| || |  || ||||||||||| || || ||||| ||||| ||||||||||| ||| |||| ||||| || ||| | |
gtaatatcgtgag------gcctctgatgtttcctaattactgttacctagtcttaagatgttaacatatctctctc-----ctttttct--cagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 3
gtatgctctttagctgctaacct-taaatgcatcctctcaatttttgctgaatttttaat-gattatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC
|||   | | |   | || |  | |  || ||| | | | |||   ||||| ||  || |  |||||   |      |  | || ||||||    |||| |||||||| ||||||||||| || |  || || |||||||||||||| ||||| ||||| || ||||| || ||| |||||||||| || ||| |||
gtaaattttctgctttcttatttcttgatccatgccccctatt---gctgatttcatacttaattataggtgtgatgtgtttcttttttgc----agGAGTTTAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAACAAGGCTTCCCAATGAAGCAAGGAGTTCTGACTTCTGGTCGTGTCCGCCTTCTGC

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatgattatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC
||| ||  ||   |   |    |  |||||      || | | |      |  ||||   |  || ||||    ||  |    || ||   |||||||||||| |||||||| |||||||| |  ||||| |||||||| ||||| ||||| ||||| ||||||||| | ||||||||||||||| | || ||||
gtaagcattt--accattgttatgcaatgccaaaattctactatcagactagatttatataacatttatttttgtttgtttgtttgtgt-gacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC

upper sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3
gtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatgattatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC
||||||  |||  |||||   ||   |   ||       || ||   |||   | || | || ||  |       ||||   |||      |||||| || ||||||||||| ||||| || |  || ||||||||||| ||||| || || ||||| |||||||| || |||||||| |||||| | |||||||
gtatgcctttt--ctgctcttctcccacttatttatctcatattgtttga---tctactaatcatacaaaacatgtcatctgcttc-----acagGAGTTCAAGGGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGC

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|209699698|gb|BW652083.1|BW652083
EST:     TTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAG                         GAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAGgtatgctctt ... ttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
EST: gi|6482119|gb|AW201390.1|AW201390
EST:     TTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAG                         GAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAGgtatgctctt ... ttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
EST: gi|308097910|gb|HO761081.1|HO761081
EST:     CGGAGATGCACTTGGTGAG                         GAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
genomic: CGGAGATGCACTTGGTGAGgtatgctctt ... ttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
EST: gi|192296729|gb|FG991297.1|FG991297
EST:     TTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAG                         GAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
genomic: TTTGGGACAAGAGGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAGgtatgctctt ... ttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
EST: gi|298187174|gb|HO034323.1|HO034323
EST:     GGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAG                         GAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA
genomic: GGATCTCACAGGAGGTCAGCGGAGATGCACTTGGTGAGgtatgctctt ... ttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgctgaatttttaatgattatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC
            ttttaat  putative branch site (score: 3)
                                ccttcatgctctttt  putative PPT
       tgaatttttaatgatt  TA-rich tract