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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcatatgatgaatcttgcctgtgattctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG

Basic information

species Glycine max
transcript GLYMA08G47680.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
lower sequence: AT3G13670.1 (Arabidopsis thaliana), 3'ss of exon 12
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcatatgatgaatcttgcctgtga-----ttctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG
      || | |||| | | |   | |||        |||  |||  | | |||| |   | ||||| |||| |||| ||     ||||||||    |||||||||||| ||||| ||||||||||||||||| ||||||| ||||||||| || || |  ||||| |||||  | || || ||||||||||
-----gttgtctgatgtttctctgttagt--------tatttttatatctgtgttctgtcaagatga-tcttacctgagagtgaattctgttttgaatcagGAATGGATTATGGAGCAGTGGGAGAAGAACTACTACATTAGTTCTATTGCTGGTGCAAGCAATGGAAGCTCCTTAGTTGTCATGTCAAAAG

upper sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 12
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcata-tgatgaatcttgcctgtgattctgtttct----tttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG
|||| |||   || | |   ||  |   ||  | | |  || |||  | |   |  | ||| | || |   |    |  |||  | |||||    |  ||||||||||| |||||||| ||||||| ||||| ||| || | ||| ||||| || ||||| ||||| || || || || |||||||| ||||
gtgatattc--tggtgtccatagttttttattttttaattagttaatt-ttaataataataataataataataatttaggatcatttttctgacataccagGAATGGATTATGGAACAATGGGAGAGGAACTTTTATATCAGTTCCATTGCTGGTGCTAACAATGGAAGTTCCCTTGTTGTGATGTCCAAAG

upper sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 9
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcatatgatgaatcttgcctgtgattctgtttcttttca--gGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG---------
                                 ||  ||   ||  | |     |||  |  || |  |||  | | |   |||| | | | |||  ||||||||||||||| ||||||||||||||||| ||||| |   | || || || || || || || ||||| || ||||||||||| || |         
---------------------------------gtactacttttgacgaaacaattt--ttcgaggcttctcacattt--ctctgctgcctgtcaaagGAATGGATCATGGAGCAGTGGGAGAAGAACTACTACATCAGCGCAATCGCCGGTGCCAACAACGGTAGCTCGCTGGTGGTGATGTCCAAGGGAACGTCCT

upper sequence: GLYMA08G47680.3 (Glycine max), 3'ss of exon 10
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 10
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagc-tatctgttttcatatgatgaatcttgcctgtgattctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG
                                          |||||  ||||   || |  | |  ||||||  |   | |  |  | ||   ||||| |||||||||||||| |||||||| ||||  ||||||| | | |||||||| || || || || ||||| || || || ||||||||||
-----------------------------------------gttagcacatcttgcttaactttagtaatctt--catagctcattctcctcggcagGAGTGGATCATGGAACAATGGGAGAAAAACTTCTACATTAGTGCCATTGCAGGAGCCAACAACGGCAGCTCGCTGGTTGTCATGTCAAAAG

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|15664134|gb|BI701505.1|BI701505
EST:     CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACA-G                         GAATGGATCATGG
genomic: CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaaattat ... ttcttttcagGAATGGATCATGG
EST: gi|17023915|gb|BM094949.1|BM094949
EST:     CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAG                         GAATGCATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
genomic: CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaaattat ... ttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
EST: gi|15203977|gb|BI426754.1|BI426754
EST:     CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAG                         GAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
genomic: CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaaattat ... ttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
EST: gi|7796847|gb|AW782241.1|AW782241
EST:     CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAG                         GAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
genomic: CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaaattat ... ttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
EST: gi|14259120|gb|BG882028.1|BG882028
EST:     CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAG                         GAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
genomic: CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaaattat ... ttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
EST: gi|15287222|gb|BI471113.1|BI471113
EST:     CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAG                         GAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA
genomic: CTGGCTTTTCAAGTCAAGTTTATAAGTTGTCACCATTTTTCTTACACAAGgtgaaattat ... ttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attagctatctgttttcatatgatgaatcttgcctgtgattctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG
                                       ttctgtttcttttc  CT-rich tract
            ttttcatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaattatatgatttatgtaaatcagtacatgtcatataattagctatctgttttcatatgatgaatcttgcctgtgattctgtttcttttcagGAATGGATCATGGAACAGTGGGAGAAGAACTATTACATTACTTCTATTGCAGGGGCTAATAATGGGAGCTCTCTCGTGGTGATGTCAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT