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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtatatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 5'ss of exon 7
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtata-tgcgtttctctatcttttttg---tttccaggtg-atgataagatatgtattttctcaattgatttacag--------
||||| |||||||| ||| |||||||||| ||  |||| |||||||| ||||| || ||||||| ||||||| | ||||||||||||||  | |||||||||         ||  | | | |||| |||| ||  |  |   |  ||  ||| | | | |     || ||     ||  | || ||||| |    ||  | ||   |||   |||            
AACAAGCTTAGAGGGTCATTGAAAATTGCCGCTATCAAAGCCCCTGGTTTTGGTGAGCGCAAGACCCAGTACTTGGATGATATTGCCATTCTAACTGGAGgtgaggtggacttgcgatctggtgcatttggttgggtgatcattaatgctgcttatttatgatgattctggagcatctggctggatgattaatgctgcttatttataatgattttttttctctgcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 7
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgt-----gcctttgattttggaagtgtgtatatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag
||||  ||||| ||  || |||| ||||| ||  | || || ||||| |||||||| |||||||| || ||||||||||||||||| |   | |||||||||      ||||| || |||||      |   |  |   |  |||     |  |||| || | |||| || || ||||                                         
AACAGGCTTAGGGGTGCATTGAAGATTGCTGCTATTAAAGCTCCTGGTTTTGGAGAACGCAAGAGTCAATACCTTGATGATATTGCTACTCTTACTGGAGgt-----gatattcagcttttgacataagttgtctacactctaagc-cacacgtgcgcttatatatcgttcttctttcag---------------------------------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 1
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgta-tatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag
||||| || ||||||||| |||| ||||| ||  |||| |||||||| |||||||| |||||||  |||||| | ||||||||||||||| | ||||||||||  | ||  ||  ||| | | || |    || ||    ||| |  |    |||| |     || ||||||||                                         
AACAAGCTCAGAGGATCATTGAAGATTGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagttaaacttccgttctagagcatcc--ttatgatcatgtatgctccttgtttataagcattctttgtttctgcag------------------------------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 6
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtatatgcgtttc-tctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag
||||| || |||||||||||||| || || ||  |||| |||||||| |||||||| |||||||  |||||| | ||||||||||||||| | ||||||||||    ||  ||   || |   || |   ||||||    ||| |  |     | | |  |  |  ||||||||                                         
AACAAGCTCAGAGGATCACTGAAGATCGCTGCCATCAAAGCCCCTGGTTTTGGAGAGCGCAAGACTCAGTACTTGGATGATATTGCCATCCTTACTGGAGgtcagctaaacttccattctaaagcttc--attttgatcatgtatgcaccttatccataaacatactttgtttctgcag------------------------------------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 5'ss of exon 7
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtatatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag
||||| ||||||||  ||||||| || ||||| ||||  || || ||||||||||| ||||||||||| ||||||||||||||||||||  | |||||||||           ||||| |     | |||||    |   | ||| || || | | | | |  ||||| | |    ||  | ||    ||| |    |  ||            
AACAAGCTTAGAGGTACACTGAAGATAGCAGCTCTCAGAGCTCCAGGGTTTGGAGAGCGCAAGAGCCAATACCTTGATGATATTGCCATTCTAACTGGAGgt-----------aagttctgtctgcattgat--gagccctatgtttacgcatatatttgtagtttttatctt---gtcctaattttctatcttcgcttgcag-----------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 7
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtat--atgcgtttctctatcttttttgtttccaggtga-tgataagat------atgtattttctcaattgatttacag
||||| ||||||||  ||||||| |||||||| ||||| || ||||| |||||||| ||||||||||| |||||||| |||||||||||  | |||||||||      |  | | |||||| |  |    |   |  | ||| ||||  ||   | |  |   ||  ||||    ||  ||  || ||| |        |||   ||||   ||  | | |||
AACAAGCTTAGAGGCACACTGAAGATTGCAGCTCTCAAAGCTCCTGGATTTGGAGAGCGCAAGAGCCAATACCTTGACGATATTGCCATTCTAACTGGAGgt------aggtcatgtttttataacaaaaaacctatatgtgggtatcaatcaatgtgccctcctgatttggaatcatttggctgttaaaaccttaccgtgttgcttctgtttttgtgtgcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 7
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtatatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag
|| || |||||||| ||| | || ||||| ||||| || |||||||| |||||||| ||||||||||||||||| ||||| ||||| ||  |||||||||||    | | || |  ||||      |||  ||||     | |  || |   |||   |     |||| ||   |  |  ||  |  || | ||||| | ||            
AATAAGCTTAGAGGGTCATTAAAGATTGCTGCACTTAAAGCCCCTGGATTTGGAGAGCGCAAGAGCCAGTACCTGGATGACATTGCAATTCTGACTGGAGgttagcatagataacattttcac-tatttttttttcttcttctaaattttattttacttgagagttttattctaatattctgtcattat-tatatttgcaca------------

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|193593269|gb|FK548909.1|FK548909
EST:     TGGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|16278868|gb|BI943136.1|BI943136
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|193629072|gb|FK576466.1|FK576466
EST:     GGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: GGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|16278211|gb|BI942785.1|BI942785
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|209696896|gb|BW660461.1|BW660461
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTG
EST: gi|6481406|gb|AW200677.1|AW200677
EST:     TGGAGAGCGCAAGAGCCAGTACC-TGATGATATTGCCATCCTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|208146316|gb|GD948421.1|GD948421
EST:     CGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: CGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|26046015|gb|CA783382.1|CA783382
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|207757511|gb|GD729685.1|GD729685
EST:     TGGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|298192668|gb|HO033102.1|HO033102
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGGGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|24135545|gb|BU926055.1|BU926055
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGGCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|208317500|gb|GE114867.1|GE114867
EST:     GCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: GCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|16276840|gb|BI942072.1|BI942072
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|193624222|gb|FK573374.1|FK573374
EST:     TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGG
EST: gi|208230249|gb|GE031696.1|GE031696
EST:     CCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAGG
genomic: CCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|17400588|gb|BM177370.1|BM177370
EST:     TGGAGAGCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: TGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
EST: gi|208294352|gb|GE093051.1|GE093051
EST:     CATCTTGACTGGAG                         GTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG
genomic: CATCTTGACTGGAGgtctttaaat ... tgatttacagGTACTGTAATCAGAGAAGAGGTTGGCCTTACTTTGGACAAAGCTGGGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAACTTAGAGGATCACTGAAAATTGCAGCACTCAAGGCCCCTGGGTTTGGAGATCGCAAGAGCCAGTACCTTGATGATATTGCCATCTTGACTGGAGgtctttaaatattaagtttttgtgcctttgattttggaagtgtgtatatgcgtttctctatcttttttgtttccaggtgatgataagatatgtattttctcaattgatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA