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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaattacatacttgtattttattgggtttctgttgtatattaatgaatgaattttccaatttaaaattgaatccttaaaaattgtaggtaggca...

Basic information

species Glycine max
transcript GLYMA10G35960.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 5'ss of exon 3
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaatta--catacttgtattttattgggtttctgttgtatattaa----tgaatgaattttccaatttaaaattgaatccttaaaaattgtaggtaggca
 | ||  | ||||| ||||| || || ||||||||||| || || |||||  ||||||||||||| || || |||||||||||  ||||||   |  ||   | |||    | || | || ||  ||  |  ||||| |    |  ||  ||| ||  |  |     | |    | ||   || | ||      
CTCGACATTTATTCTTTGTCGAGGAAATGGAAGGAGTTAGTCGATAAGGCTCGAGCGAAGCAGCTACAGCCCCATGAATACAATTCTGgtactttctttgtccgtacacaaaattaaatgtgtagctcattgatattcaattttctatatattatctgagatggttataaggaatcaactgttcttgg------

upper sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G036534_T01 (Zea mays), 5'ss of exon 3
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaattacatacttgtattttattgggtttctgttgtatattaatgaatgaattttccaat-ttaaaattgaatccttaaaaattgtaggtaggca---
 ||||  | |||||||||||||| || ||||||||||||||||| |||||  |||| |||||||| || || ||||| |||||| |||||||  |  || |   ||  ||    | |  |  | ||  | | |||  || ||   ||||| |||  |   | | |    |     ||  ||  ||       
CTTGACATTTATTCATTGTCAAGGAAATGGAAGGAGTTGGTTGATAAGGCGCGAGCAAAGCAGCTGCAGCCCCATGAGTACAACTCTGgtatt-tctttgc---ctcatacacaaatctgaatatgcagcacattcttgcataccttttctaatactctgagtaagatgtggtcgatgctacatatttcttt

upper sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G165176_T01 (Zea mays), 5'ss of exon 5
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaattacatacttgtattttattgggtttctgttgtatattaatgaatgaattttccaat--ttaaaattgaatccttaaaaattgtaggtaggca----
 ||||  | |||||||||||||| || ||||| ||||| ||||| |||||  |||| |||||| | || || ||||| |||||| |||||||  |  || |    |  ||    | |  |  |  |  | | |||  ||  |   ||||| |||  ||  |||   ||  |  | | ||  ||  |  ||    
CTTGACATTTATTCATTGTCAAGGAAATGGAAAGAGTTAGTTGATAAGGCGCGAGCAAAGCAGTTGCAGCCCCATGAGTACAACTCTGgtatt-tctttgc---ttcatacacaaatctgaatacgcagcacattgttgtgtatcttttctaatgttttgaataagattgt--atacttacagagattcactta

upper sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G34430.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgta----tagtaattacatacttgtattttattgggtttctgttgtatattaatgaa------tgaattttccaatttaaaattgaatccttaaaaattgtaggtaggca
 ||||  | ||||| || || ||||| ||||| || |||||||| |||||  |||| |||||||| || ||||| || |||||||||||||    || || |   ||| ||| | |   ||| ||||  ||  |   | ||  |       ||| | ||    |||  | ||   | |     ||||| ||       
GTTGACATTTATTCGTTATCTAGAAAATGGAAAGAATTGGTTGATAAGGCTCGAGCCAAGCAGCTGCAGCCTCAGGAGTACAACACTGgtaatcctactactagaata-ttgaagtgatttgagtttgagtaatccttcaactagattgtttgagtcttgttgtttttatttcccttccgggtaattgcag-------

upper sequence: GLYMA10G35960.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv18s0072g01000.t01 (Vitis vinifera), 5'ss of exon 3
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaattacatacttgtattttattgggtt-tctgttgtatattaatgaatgaattttccaatttaaaattgaatccttaaaaattgtaggtaggca--
 | ||  | |||||||||||||||||||||||||||||||||||||||||| |||| |||||||| ||||||||||||||||| || |||||  | ||||||| ||      | |||   |  |      | | |   ||    |   ||      | | ||  |    ||| |   | ||| ||| ||  
GTGGACATTTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCCGAGCAAAGCAGCTGCAACCTCATGAATACAATACAGgtatcctcattacatcctacacactcattacatcatacaagatgtttccttgtgcaataattgatggctcatatctatatattaga---tatagatagacacc

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|13790727|gb|BG653318.1|BG653318
EST:     GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
genomic: GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
EST: gi|208057351|gb|GD850900.1|GD850900
EST:     GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTT
genomic: GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTT
EST: gi|193417002|gb|FK382036.1|FK382036
EST:     CGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
genomic: CGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
EST: gi|208235385|gb|GE029669.1|GE029669
EST:     GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTG                         GTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG
genomic: GGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaat ... ttttttatagGTACTTTCACTCTGTCCAATCTGGGAATGTTTGGTGTTGATCGCTTTGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATGTCTATTCATTGTCAAGAAAGTGGAAGGAGTTGGTTGACAAGGCCAGAGCGAAGCAGCTTCAACCTCATGAATACAACACTGgtatagtaattacatacttgtattttattgggtttctgttgtatattaatgaatgaattttccaatttaaaattgaatccttaaaaattgtaggtaggca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT