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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctctggatttattgtgttacttgtggaacag

Basic information

species Glycine max
transcript GLYMA01G36880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 5'ss of exon 3
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatg-ctgcgtgat-----tattgtttctgtgatgttggagcttggaagttttc--tctggatttattgtgttacttgtg-gaacag
|||||||| ||||||||||| || || || ||||||||||||||||| |||||   || ||||||||| ||  | |||||||| || |||| || ||   | ||     | ||  ||    |  |  | ||||  |   |||    |||| |  | |||| ||  |  ||  |||||
GATTATGTACCGACTGTTTTCGATAACTTTAGCGCAAATGTGGTTGTTAATGGAGCCACTGTGAATCTTGGGCTATGGGATACCGCAGgtactgactaaataatagggatcttacttagtagtagcggcagctatgggatttggggtctgaaacttttgttttgttgttgtaaacag

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 5'ss of exon 2
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgcgtgatt--attgtt--tctgtgatgttggagcttg----gaagttttctctggatttattgtgtta-cttgtggaacag
|||||||| ||||||||||| || || || || |||||||||||||| |||||   ||  |||||||| || |||||||||||||| |||||||     ||||   |||  |  ||  || ||   ||||||     || |  |     | | ||||  | ||   || || |    
GATTATGTTCCGACTGTTTTCGATAACTTTAGTGCAAATGTGGTTGTTAATGGAGCCACGGTGAATCTTGGATTGTGGGATACTGCAGgtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcag---

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 3
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaat------gctgcgtgatta-----ttgtttctg--tgatgttggagcttggaagttttctctggattt-attgtgttacttgtggaacag
||||||||||| |||||||| ||||||||||| |||||||||||||||||||||  || ||| || || || |||||||||||||||||||        |   | || ||      ||||||     |  |     |  ||   | | || | ||| | | | | ||||   | ||||||||
GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacag

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctctggatttattgtgttacttgtggaacag
||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || ||  | ||||| |||||||||    |      |    ||| | ||   ||  |  |  |  |  | |  |||     |  |  || ||           
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcag-------

upper sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ09765 (Selaginella moellendorffii), 5'ss of exon 2
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctctggatttattgtgttacttgtggaacag
||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || ||  | ||||| |||||||||  |  |     |  | | | | | ||| | || | |    |  | |  |||     |  |  || ||           
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgt--tcgtcaaaaaaaaatctgtgtttgaggatgaatc---aatctctcatctctggctgcttcgtcacgcag-------

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|26268044|gb|CA819107.1|CA819107
EST:     GAGCATTGTGATTCTGCCTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: GAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|26057126|gb|CA800040.1|CA800040
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|298166464|gb|HO009903.1|HO009903
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|298183384|gb|HO028597.1|HO028597
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|19452394|gb|BM953804.1|BM953804
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|5175630|gb|AI759963.1|AI759963
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|10843808|gb|BF067063.1|BF067063
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|17964056|gb|BM270797.1|BM270797
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|7925509|gb|AW831535.1|AW831535
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|5688224|gb|AI941239.1|AI941239
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|37995833|gb|CF807422.1|CF807422
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|7684704|gb|AW755352.1|AW755352
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGCGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
EST: gi|21602816|gb|BQ613147.1|BQ613147
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GGCAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGT
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGT
EST: gi|17964054|gb|BM270795.1|BM270795
EST:     TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTG                         GACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG
genomic: TGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgc ... tgtggaacagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctctggatttattgtgttacttgtggaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA