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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaaaagttcaaatatcaacctgggatacaaattctactggtgttctaattat...

Basic information

species Glycine max
transcript GLYMA18G04170.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04170.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 4
-TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaaaagttcaaatatcaacctgggatacaaattctactggtgttctaattat
 |||| ||||||||||||||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||| ||  ||| |||||     || |||  |  | |  |   |   || | |||         ||  | |  | || | |   |      | | | |             
GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgt-ctgtt-----gctatttctcctatgcg---atgcaaatttgagttcctggtgtctataattgaatcagctttgt---ctttgcag-------------

upper sequence: GLYMA18G04170.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g62610.1 (Oryza sativa), 5'ss of exon 6
-TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaaaagttcaaatatcaacctgggatacaaattctactggtgttctaattat--
 ||||||| |||||||| || || ||||||||||||||||| |||||   |||||| || |||||||| || || ||||||||    ||| |   | |    | |   | | ||  |   | ||        | || || |  ||||   |  | | |||     ||| | || |    |   
GTTGGAGAGGTTGCAAAGATCACATGCAAGCCAGAATATGCTTATGGAGCTGCAGGTTCACCTCCAGAGATACCGCCAGAgta--agtctgaaaacttgatctgtcactagtaaagt--ctttggtttttttatgtacagagttcaaag-gtaacagaaacagctctgtttttttttccacag

upper sequence: GLYMA18G04170.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 5'ss of exon 4
-TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaaaagttcaaatatcaacctgggatacaaattctactggtgttctaattat
 ||||||||||||||||||| || || |||||||||||||| || || || || || |||||||| || || || || |||||    | | |||      | ||   ||| |         | | |     | ||||    | |     | | |    |  | |   |   ||  |     
GTTGGAGAAGTTGCAAAAATTACATGTAAGCCAGAATATGCTTACGGAAGAGCCGGGTCTCCTCCCGACATCCCACCTGAgta----tgttatgttccaaacttc--ttgcatctcgttcaagggagtgtgacagttttttttttgtttttgtaattgagatttttggtaattgcag----

upper sequence: GLYMA18G04170.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 5'ss of exon 4
-TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaa-aagttcaaatatcaacctgggatacaaattctactggtgtt--ctaattat--
 |||| || ||||||||||| |||||||||||||| || ||||| ||   ||| || ||||| |||||||| ||| ||||||| | || | |        ||  ||| |     |||  |||  | ||||   || || || |||     |    || || |   ||    | |  | ||  ||  
GTTGGGGAGGTTGCAAAAATCACTTGCAAGCCAGAGTACGCATACGGAGCTGCTGGTTCTCCACCAGATATCCCTGCAGAgtaatatttttact------atcctgtctcctgtcattgttagaacacaagccaaatttaattattctgtttaagtagaagtaaaacataagatgcccaagcattg

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|298193802|gb|HO040450.1|HO040450
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
EST: gi|298188914|gb|HO035607.1|HO035607
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
EST: gi|5676869|gb|AI937999.1|AI937999
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGT
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGT
EST: gi|298175755|gb|HO018352.1|HO018352
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAG
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAG
EST: gi|21887331|gb|BQ740544.1|BQ740544
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
EST: gi|298169599|gb|HO020959.1|HO020959
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
EST: gi|298171704|gb|HO021296.1|HO021296
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
EST: gi|298185077|gb|HO030290.1|HO030290
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTTCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCC
EST: gi|298169647|gb|HO021007.1|HO021007
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
EST: gi|18726884|gb|BM523811.1|BM523811
EST:     CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAT                         GCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC
genomic: CAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctc ... cccttgcagtGCAACACTTGTTTTTGAAGTTGAGCTAGTTGCCTGTCGGCCAAGGAAGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGAGAAGTTGCAAAAATAACTTGCAAGCCAGAATATGCATATGGTAGTGCAGGATCTCCTCCAGATATTCCTCCAGAGtactgttctcatgccattgattttgtttggaaacataattatgaaacaaaaaagttcaaatatcaacctgggatacaaattctactggtgttctaattat

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaaa