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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccttttatgaaagaatttaaaagatgaaattatgtttaatttatgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG

Basic information

species Glycine max
transcript GLYMA20G28200.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 16
ctccttttatgaaagaatttaaaagatgaaattatgtttaatttatgtcagctgtagctt--tgttatgc-ctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
    |      ||| || |  |    | |  ||    | || |  |||    | | || |  | | |  | ||  |      | |  ||||    | |||||||||| || ||||||||||| ||||||||||| || || ||||| ||||| ||  |||| ||||| ||||||||||| |||||  |     | |||   ||
---ttaaccccaaataagtctaggtttcatcttcaactaaaatattgtttttttttgcgtgctatcacactctcataatgtaaatcctgttgccatttttcagAGATTAAGCTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATCAACCATATCCTCGTGGAGAAATTTGTGTTAGGGGAACTACGATATTTTTTGG

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 15
------------------------------------------------ctccttttatgaa-agaatttaaaagatgaaattatgtttaatttatgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
                                                 ||||||| |  | || | ||      ||  ||| | |||      | |||  | |  |  | ||     ||  || ||   || ||||  | | |||||||||| |||||||||||||| ||||||||||| || || ||||| ||| | ||  |||| ||||| ||||| ||||| ||||| ||     | ||  | ||
gtaagatctgtgtttgggtttaactagacttggttggataaataacttgtccttttgttcacagtaattcctcactgttattgtttttgtacattatcacttctcacactcttcca--taacgcaaa---ttctgtttctatttttcagAGATTAAACTAGTGGATGTCCCAGAAATGAATTACACCTCTGAGGATGAACCATATCCTCGTGGAGAAATCTGTGTTAGGGGACCTACGATATTCTGTGG

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 7
ctccttttatgaaaga-atttaaaagatgaaattatgtttaatttatgtcagctgtagctttgttatg----cctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
    |   |||| |   || |  || ||  ||||  || |   ||    |   ||||   |||| |      | || ||   |   || ||||    | |||||||| | ||||| |||||||| ||||||||||| ||||||||||||||||| ||  |||| ||||| ||||||||||| || || ||  |  | || |  ||
--aatcaaatgacatccatatccaaaat--aattgggtgtgcctttgtgcttttgtattattgtcacagtttcgtaatgtggatctttgtgtttccat-tttcagAGGTGAAACTTGTGGATGTCCCAGAAATGAATTATACATCTGATGATCAACCTTATCCTCGTGGAGAAATTTGTGTTAGAGGACCTATAATATTCCAGGG

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 16
ctccttttatgaaagaatttaaaagatga-aattatgtttaatttatgtcagctgta-gctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
 |    || | |  || | |   | |||| || ||   | | ||      |  | |    |||    ||| | | |     |  |   ||  | | |||||||  |||| || |||||||| |||||||||||||||||||| |  ||||||||| |||||||||| ||||| ||||| ||||||||  |  |||||  |||
gtgagctttttactgactctgcgatatgataagtagagtaatttggaactaaatatccattttaaattgctttgggatttaatatgcatttctatatttcagAAGTAAAGCTTGTGGATGTCCCAGAAATGAACTATACATCAGCGGATCAGCCCCATCCCCGTGGCGAAATATGTGTTAGGGGTCCTATCATTTTTACAGG

upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 16
ctccttttatgaaagaatttaaaagatga-aattatgtttaatttatgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
  |     |     |  |    |  |  | |||| | |||   || ||     ||  ||| | || ||          |  |||   || |  | |||||||  | || || ||||||||||| ||||||||||| |||||||| ||||||||| |||| ||||||||||| |||||  |||||||| || |||||| |||
aacaagaaaaatgtggctcctgagtacaacaattttctttccattgtggtctgtgctgctctattttgggataaatttat-gttaatttgtcctctttcagAAGTGAAGCTTGTGGATGTTCCGGAAATGAACTACACATCTGAGGATCAGCCCTATCCTCGTGGTGAAATCTGTGTTCGGGGTCCCATTCTTTTTCTAGG

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|16349014|gb|BI974609.1|BI974609
EST:     TGAGGGTGACAAACTTGGTGGTCATGTAGGCTCTCCTAATCTAGCCTGTG                         AGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGC
genomic: TGAGGGTGACAAACTTGGTGGTCATGTAGGCTCTCCTAATCTAGCCTGTGgtgagtactt ... tttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGC
EST: gi|151400349|gb|EV270163.1|EV270163
EST:     TGAGGGTGACAAACTTGGTGGTCATGTAGGCTCTCCTAATCTAGCCTGTG                         AGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGC
genomic: TGAGGGTGACAAACTTGGTGGTCATGTAGGCTCTCCTAATCTAGCCTGTGgtgagtactt ... tttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG
                                    ttttgttcttttgttt  CT-rich tract
             tttgttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccttttatgaaagaatttaaaagatgaaattatgtttaatttatgtcagctgtagctttgttatgcctagtgccaacagttttgttcttttgtttcagAGATAAAACTAGTGGATGTTCCAGAAATGAACTATACATCTGATGATCAGCCCAATCCCCGTGGTGAAATTTGTGTCAGGGGTCCCCTTGTTTTTCGAGG

- - - - - - - - - - - - - - - - - - - - - - - - cagctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccaac