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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcattcatgaatggtttttcaaaaaccattcttatatgtttatttattatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

Basic information

species Glycine max
transcript GLYMA17G14450.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
ccttcattcatgaatggtttttcaa--aaaccattcttatatgtttatt-tattatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
  || |||     |||  | || |     |  | ||   | ||||| |  | || |  | ||| | |  | ||   | || |   |  ||  | ||     |||  | | || || || || |  || || ||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| || || ||||| |||
-atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaatta--ccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG

upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os04g18030.3 (Oryza sativa), 3'ss of exon 14
ccttcattcatgaatggtttttcaaaaaccattcttatatgtttatttattatcta-gttactgtcatcataaactttacacaac-------tttgcatttcattt---agAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
          | |||||| || |||| |    | |||| | |  ||| ||||| |  |||  |   ||| |   ||||    ||         |||  ||  ||||   |||  | |||| ||  | ||||| |  || ||||| || ||||||||||| ||||| || ||||| || ||||||||||||||  | || ||||| |||
---------gttaatggtatt-caaagatttgttttatgt-tgaattaattatttctgttgataggatccttttctttttgtaatgtaaatgcttgtgttatatttgtcagAAATGGTGGAGATTTATCAACCAAAGAGTTGCAAAAAATGGTTCAAGCTCTTCCGCAGTACAGTGATCAAATTGACAAGCTTGCGCTTCATGTTGAG

upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G012942_T01 (Zea mays), 3'ss of exon 12
ccttcattcatgaatggtttttcaaaaaccattc-ttatatgtttatttattatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
         |  |||| | ||    |||  |||   |   || |   |   |   | | |   || | |||  | || | |  |  |    |     | |||  | |||| ||  | || || | | | |||||||| ||||||||||| |||||||||||||| || ||||||||||||||| |||| ||||| |||
aaagggccaagcaatgctgttagctaaagtattagctgcttgatagctgtgtcaatggatctggttaacattta-ttcataggatctattttgagtgtcagATCTGGTGGAGAGTTATCTACCAAGCAGTTGCAGAAAATGGTTCAAGCTCTTCCACAATACAGTGATCAAATTGACAAGCTCACCCTTCATGTTGAG

upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
ccttcattcatgaatggtttttcaaaaaccattctt-atatgtttattta--ttatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
| | ||||  |  | | |  |  |      || ||| || || |||   |  |        |    |  | || || |||     ||| |   |||   |||||| | | | |||  | || ||||| || ||||||||||||||||||||| | ||||| ||||| |||||||||||||||||||| ||||| ||||||
cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactct---tttttcttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG

upper sequence: GLYMA17G14450.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
ccttcattcatgaatggtttttcaaaaaccattcttat--atgtttatttatt--atctagttactgtcatcataaactttacacaac-tttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
  |  ||   ||  || | | |    || | ||||  |  |||    | ||||    | ||| |    ||  ||    |   |  ||  |||   | | || ||||||| |||||||| |||| |||||||||||||| ||||||||||||||  | |||||||| || || |||||||| ||||| ||||||||||| |||
-atgtatctttg--tgatatctggttaatctttctacttgatgccagtgtattcagaccagtaatc--caggatgtgttaacctaaatatttatctgttatgtagAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG

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|254321302|gb|GR824619.1|GR824619
EST:     ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG                         AGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
EST: gi|213600619|gb|DB956179.1|DB956179
EST:     ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG                         AGGTAGTGGTGAAATGTCAACAATGGACTTGCAGAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
EST: gi|308098914|gb|HO760755.1|HO760755
EST:     GCCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG                         AGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
EST: gi|208084886|gb|GD881084.1|GD881084
EST:     ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAG                         AGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
genomic: ACCAACTTCATTTCAAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
EST: gi|208338305|gb|GE139691.1|GE139691
EST:     AAAGAAT-AAGCTGCACAAATCCAACATGGTTCAAG                         AGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT
genomic: AAAGAATAAAGCTGCACAAATCCAACATGGTTCAAGgttagtctta ... tttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG
                                             tttcattt  CT-rich tract
                       ataaacttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcattcatgaatggtttttcaaaaaccattcttatatgtttatttattatctagttactgtcatcataaactttacacaactttgcatttcatttagAGGTAGTGGTGAAATGTCAACAAGGGACTTGCAGAAGATGGTTCAAGCACTTCCACAATACAGCGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
ccttcat
- - - - catgaat
- - - - - - - - - - - - - - ccattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctttgca