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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttatcttctattctttgtagattcttgatactatttatctcttttgggttgttgattttactatgaaaagatgatgctaattggtattttgttgctgcctcatag

Basic information

species Glycine max
transcript GLYMA10G26890.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 5'ss of exon 5
AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttatct--tctattctttgtagattcttgatactatttatctcttttgggttgttgattttactatgaaaagatgatgctaattggtattttgttgctgcctcatag
 || ||||| |||||||| ||||| || |||||||||||||||||  | ||||| ||    || ||||||||||| || |||||||| || ||||||||||||| |  ||    || || | ||  |      || | || | |   | |  | | |||   |||||  | | | ||| || | ||  ||   |                   
TGCTAAATCCATGAAGTTCAAGGACGGATACATGATTTCTTCTGGTTATCCTGTTAACTTGTATATTGACTCTGCTGTTAGACATGTTCTTCTGAGACAGgtttgtacataaaatccatccgtttgaataaaatgttgctgtctccttgtgatagcttg--aatttttttcttagaagctgcttcttgttttcag------------------

upper sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G093902_T02 (Zea mays), 5'ss of exon 5
AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttatcttctattctttgtagattcttgatactatt-tatctcttttgggttgttgattttactatgaa-aagatgatgctaattggtattttgttgctgcctcatag
 || || ||||||||||| |||||||||||||||||||||||||| || ||||||||    |||||||| || || ||||||||||| ||  ||||||||||||  |    |  |||    |||    |  | || | |   |||  |      | ||||  |  |||| |     |  ||     |                          
TGCTAAGTCTATGAAGTTCAAGGATGGGTACATGATTTCTTCTGGTCATCCTGTCAACCTATACATTGATTCAGCTGTGAGACATGTTCTATTGAGACAGgtttggt-gcttggtatcagatgttatcttattatgcaaacatataacaaaatagctgttagtaatactctagttgacttggcttcag-------------------------

upper sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G53870.1 (Arabidopsis thaliana), 5'ss of exon 4
AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgt---ttttttatcttctattctttgtagattcttgatactatttatctcttttgggttgttgattttactatgaaaagatgatgctaattggtattttgttgctgcctcatag
|||||| ||||||||||| || ||||| |||||| | || ||||| |||||    || || ||||| ||||||||||||||||||||  | || ||||| ||   |||  | |    | |||||  |||| |   |  |  | | | |    |    ||   |  ||    |    || |||  |                             
AGCCAAGTCTATGAAGTTCAAAGATGGCTACATGGTGTCATCTGGTCAACCAACTAAGGAATACATAGACTCTGCAGTGAGACATGTTTTGCTTAGACAAgtgagtttcgtctgagttgttcttattagagttaagtaaaaaatcaacaacgtctaattaaagtgttgttaaaccgaatatgtag-----------------------------

upper sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv11s0016g01380.t01 (Vitis vinifera), 5'ss of exon 5
AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttatcttctattctttgtagattcttgatactatttatc--tcttttgggttgttgattttactatgaaaa--gatgatgctaattggtattttgttgctgcctcatag----------------------
 |||||||| |||||||||||||||||||||||||| |||||||| || || ||||| || || |||||||| || |||||||||||||| || ||||||||||  ||  ||       ||  |   ||| || | || ||| |     |  |      |||   |   |   |     | | |   | ||||  ||| |||      |   |                        
TGCCAAATCCATGAAGTTTAAGGATGGGTACATGATATCTTCTGGTCAGCCAGTCAAGGAATATATTGACTCAGCTGTGAGACATGTGCTTCTAAGACAGgtttgcttcactcacccagttgatctgttcatgcttctttttgttaacatcctcaaccattgcggtggttcatacggttgcttaccttcattgcaattgtgtcctgatcatgttctggattgcttgccatcaaacag

upper sequence: GLYMA10G26890.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 5'ss of exon 5
AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttatcttctattctttg-tagattcttgatactatttat-ctcttttgggttgttgattttactatgaaaagatgatgctaattggtattttgttgc--tgcctcatag-----------------------
|||||| ||||||||||| |||||||| ||||||||||| || ||    || ||||| |||||||| ||   ||| || ||||| ||  |  |  ||||||||| |  | |  ||||||  || |    |||   |  | |   | ||  |||    |   |  |||  | | || | |  ||     |||  | ||   ||   ||  || |||                       
AGCCAAGTCTATGAAGTTCAAGGATGGCTACATGATTTCATCAGGAAGCCCCGTCAACGATTACATCGATAGTGCTGTCAGACACGTCATGTTACGACAGgtttgtcgagcagctattcagtggtgtcctctctgtggtctccttgctgatttctcctacggtctttgttttcaagaaaaaatctcgtttgcaagttgtctgtaatgtatcttagaaatgtttcgttatttttttcag

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|21256674|gb|BQ453562.1|BQ453562
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGACACATGTGCTCCTGAGACAG                         TGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|298195932|gb|HO044323.1|HO044323
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|33387986|gb|CA851193.1|CA851193
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|7590784|gb|AW706456.1|AW706456
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|15813066|gb|BI785341.1|BI785341
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAA-TGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|21256892|gb|BQ453780.1|BQ453780
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAT                         TGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|6726858|gb|AW311277.1|AW311277
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|21993919|gb|BQ785447.1|BQ785447
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
EST: gi|6725216|gb|AW309615.1|AW309615
EST:     CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAG                         GGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG
genomic: CTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttat ... tgcctcatagGGTGTTCTTGGCATTAAGGTGAAGATCATGCTTGATTGGGATCCTAAGGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAAATCTATGAAGTTTAAGGATGGGTACATGATTTCTTCTGGGCAACCTGTCAAAGATTACATTGACTCTGCAGTGAGACATGTGCTCCTGAGACAGgtttttttatcttctattctttgtagattcttgatactatttatctcttttgggttgttgattttactatgaaaagatgatgctaattggtattttgttgctgcctcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG