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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccag

Basic information

species Glycine max
transcript GLYMA07G36680.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
lower sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccag
|||| ||| | || ||||| ||||| || || || || ||||| ||||| || || ||||| || |||||||||||||||||||||||||| || |||||||| || |    |  |||||  |   ||   | |  || ||| |||  | |  |  | ||  ||| ||  ||| |  |  |  |  |||
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtatt--accaaaaatgtaattttcttctgattgtttcag

upper sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
lower sequence: AT1G44900.1 (Arabidopsis thaliana), 5'ss of exon 9
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccag
|||| |||||||||||||| |||||||| ||||| ||||| || |||||| |||||||||||||||| |||||||||||||||||||| |||||||| |||||| |||||  | ||  | |     | | |||||| ||  | ||  |             | |     || ||  ||||||| |||||
CAGTTACAAGGGAGTGGACGCTTGAAGGAGGGGCTCTTGTACTTGCTGACCGAGGAATTTGTCTTATCGATGAGTTTGACAAGATGAACGACCAGGACAGgtaacaaaatgcaactaatga--tagttacttttctgaaggaaatggt-----------gctgac---gatataagtttttgtaaccag

upper sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 5'ss of exon 10
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgacct-tgtaaatccttgagttttc-ttaattacattattatccttgatcattaatttatatttatatttttgttaccag
| |||||| | || ||||| |||||||| ||||| ||||||||||| || | |||||| ||||| |||||||||||||||||||||||||| || || ||||||| ||||  |  |  ||| ||  | |   ||   |   || ||  | | |   | ||  | ||     |  | ||| |    ||  ||
CTGTCACACGCGAATGGACACTTGAAGGAGGGGCTCTTGTTCTAGCAGATAAAGGAATCTGTCTAATTGATGAGTTTGACAAGATGAATGATCAAGACAGgtaaggaaatgtatgtgcgtatattttggtacttcaatcccttgcaaaaatttgtatcat-gtgaacaagaaagtttatatcctctattag

upper sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
lower sequence: PP1S28_266V6.1 (Physcomitrella patens), 5'ss of exon 10
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattacat---tattatccttga-----tcattaatttatatttatatttttgttaccag---------------------------------------------------
| || ||||||||||||||| | ||||| || || ||||| ||||||||| | || || ||||||||||||||||| ||||||||||| || || || ||||  | |         || | || |   | ||||| |||  |  |   ||   | |||||     ||| |     |   ||| |     | | |  |                                                   
CTGTAACAAGGGAGTGGACTTTGGAAGGAGGTGCCCTTGTACTAGCTGACCGTGGTATATGTCTTATTGATGAGTTCGACAAGATGAACGATCAAGACAGgt--gcagtccctttctggagatgc---atttttcataaccatttgtatacagttcttgaaactctcaattgccaagccttagaaaaacgctccttgatgtgctgctatttcatctgaagactttgtgtgaaattcgattttgtttag

upper sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ31227 (Selaginella moellendorffii), 5'ss of exon 7
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaa---gaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccag
| || ||  | ||||||||  | ||||| || ||  | ||  | || ||  | ||||| || || ||||||||||||||||| ||||||||||| || |||||     ||    |  |||  ||   |||      ||   | ||  || | |                                       
CTGTAACTCGCGAGTGGACATTAGAAGGCGGCGCCTTGGTCTTGGCCGATCGTGGAATCTGCCTCATTGATGAGTTTGACAAAATGAATGACCAAGACAGgtattttaaacgcagggcttacaatgtctta----ctcgggagtattttttcag--------------------------------------

upper sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
lower sequence: EFJ17122 (Selaginella moellendorffii), 5'ss of exon 9
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattac-attattatccttgatcattaatttatatttatatttttgttaccag
| || ||  | ||||||||  | ||||| || ||  | ||  | || ||  | ||||| || || ||||||||||||||||| ||||||||||| || |||||    ||  |        |   |||   || ||||| |    | |||| |    |                                 
CTGTAACTCGCGAGTGGACATTAGAAGGCGGCGCCTTGGTCTTGGCCGATCGTGGAATCTGCCTCATTGATGAGTTTGACAAAATGAATGACCAAGACAGgtattttaaacgc-------agggcttacattgtcttactcgggagtattttttcag---------------------------------

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|15813323|gb|BI785598.1|BI785598
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|27424931|gb|CA936451.1|CA936451
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|208220913|gb|GE018049.1|GE018049
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|207844410|gb|GD814455.1|GD814455
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|193476634|gb|FK439509.1|FK439509
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGGGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|193430045|gb|FK395959.1|FK395959
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCAT
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCAT
EST: gi|193604443|gb|FK555894.1|FK555894
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
EST: gi|207730351|gb|GD708807.1|GD708807
EST:     AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAG                         GGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC
genomic: AGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaat ... ttgttaccagGGTGAGCATCCATGAAGCCATGGAGCAGCAGAGTATAAGCATATCAAAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG