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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcatttaatttactggctttgtgactaacttgtttgcgagcaaattattcccttaaatatcttttccctactttagtctaaagggaagattttgtgcag

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.2 (Glycine max), 5'ss of exon 11
lower sequence: AT5G66210.4 (Arabidopsis thaliana), 5'ss of exon 9
TAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcatttaat--ttactggctttgtgactaacttgtttgcgagcaaattattcccttaaatatcttttccctactttagtctaaagggaagattttgtgcag
|||||||||| | || | |||| |  ||||  | | ||||||||||||||| || ||||| || ||||||||    ||||| || ||||||||||||||||||  |  | ||  |   | |||||  ||  |      || | ||  || | |   | | |  |  |  ||  ||      || |   ||    |||| | |||
TAGCACACTTGACGAGGCAGAGATCTCTGACCTCAGAGATCAATTTGATGCGATTGATGTGGATAAAAATGGCGTCATTAGTCTTGAAGAGATGAGACAGgtaaaagctcatgatattttgctttaagaaca------ttactagttaaatctaggcatgatcagttaatctttatgc--atccatttggccttttttctacag

upper sequence: GLYMA16G23870.2 (Glycine max), 5'ss of exon 11
lower sequence: AT2G17890.1 (Arabidopsis thaliana), 5'ss of exon 9
TAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcatttaatttactggctttgtgactaacttgtttgcgagcaaattattcccttaaatatcttttccctactttagtctaaagggaagattttgtgcag
 |  |||||| |||| ||||||||||||||| |   ||| || |||||||| || ||||| ||||| ||||||   |||||||| ||||||||||| ||||||  | | ||      | |      | || ||   |  | |||||| |    |   ||||| ||   ||  || | |||         | || | |     
AACGACACTTGATGAGGAAGAGTTGGCTGATCTTCGAGACCAGTTTGATGCGATTGATGTTGACAAGAATGGTGTCATTAGCCTTGAAGAGATGAGGCAGgtaaaaatgaa------gacaaaacta-tacctcaatcactagcaaaattgatcaggaaata-ctaagcctgacatcagttcttgttatatatatag-----

upper sequence: GLYMA16G23870.2 (Glycine max), 5'ss of exon 11
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 5'ss of exon 9
TAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcatttaat-ttactggctttgtgactaacttgtttgcg-agcaaattattcccttaaatatcttttccctactttagtctaaagggaagattttgtgcag------------------------------------------------
 ||||| ||| |||| || ||  |||||||| | |  ||||||||||||||||| ||||| || |||||||| || |||||||| ||||| |||||||||||    |||  | || ||   | |     |   |     ||  || |  ||    |  || |  |   |  ||  | ||   | || |  |   |  | || |                                                 
GAGCACGCTTGATGATGAGGAACTGGCTGATCTTAGGGATCAATTTGATGCTATCGATGTGGATAAAAATGGCTCTATTAGCCTTGAAGAAATGAGACAGgtttttttttttctttctaattctacttttgtttctcaagcctaggatgttgcaactctacaatttaatatccatccttgaacaaatgtcagtttcatatgaacagggacttctttttccattttttcataacagagatgtttcctatacag

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|208252551|gb|GE046129.1|GE046129
EST:     CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAG                         GCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
genomic: CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcattta ... ttttgtgcagGCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
EST: gi|208260162|gb|GE059002.1|GE059002
EST:     CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAG                         GCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
genomic: CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcattta ... ttttgtgcagGCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
EST: gi|16348882|gb|BI974477.1|BI974477
EST:     CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAG                         GCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
genomic: CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcattta ... ttttgtgcagGCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
EST: gi|9204567|gb|BE330791.1|BE330791
EST:     CAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAG                         GCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
genomic: CAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcattta ... ttttgtgcagGCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
EST: gi|193432383|gb|FK394769.1|FK394769
EST:     CAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAG                         GCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
genomic: CAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcattta ... ttttgtgcagGCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
EST: gi|11274128|gb|BF324496.1|BF324496
EST:     CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAG                         GCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG
genomic: CTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcattta ... ttttgtgcagGCTCTTGCCAAAGATCTTCCTTGGAAATTGAAAGAATCACGTGTACTAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGATGAGACAGgtagcatttaatttactggctttgtgactaacttgtttgcgagcaaattattcccttaaatatcttttccctactttagtctaaagggaagattttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG