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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattgttttttataaataaatttcaattgtcatctaattgtggtccttttttaaattttagattttccaatatttcctgcagtttgttttgtttt...

Basic information

species Glycine max
transcript GLYMA08G26180.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 2
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttata-ttgtt--ttttataaataaatttcaattgtcat--ctaattgtggtcctttttta----------aattttag----attttccaatatttcctgcagtttgttttgtttt-------------------------------------------
|| || || || || || |||||| |||||||||| |||||||| |||||||||||||| || ||    ||||| |  | |||||| |||||||| ||||||   |  || ||  || | || | ||   ||| ||||  |   |||   || || |  | ||          ||   |||      |    | | | ||| | | ||  ||||  |||                                           
GGTAAAGTGAAGATCGCGGAACATATATTGACTGGTCATAAGGTGGCGATCAAGATTCTCAATCGCAAGAAGATCAGAAGCATGGATATGGAAGAGAAAGgtcattgcttattccttctgtacagaacactcatttgtggttcttaagcatgctcgtgatgtatacagtacagaaccgtagcaaagctccttattgtgtcccggaattcttttttctttgttgaagtactcaacttaatcctctcttattacgtacctgcag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 5'ss of exon 2
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatat------tgttttttata-----aataaatttcaa----------ttgtcatctaattgtggtccttttttaaattttag-attttccaatatttcc-tgca-gtttgttttgtttt-----
|| ||||| ||||| ||||| |||||  | || || ||||||||||| ||||| || ||||| || || ||||| ||||||||||| |||||||| |||||| ||||        |||  || ||     | |   ||  |           |||  |   || |||      || |||  |||||| || |     ||| |   || | || | |||  | ||     
GGGAAGGTGAAAATAGCAGAGCATGTTGTCACAGGGCATAAGGTTGCTATCAAAATCCTTAATCGTCGTAAGATCAAGAACATGGAGATGGAAGAGAAAGgtatatacaagcaccgttacttttagctttagtggtttctagaacaaaagctttgataatcaaatgtttctgcttattaggttttagtatgtatttttatcttaatgtatgtatatttcttctttacag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 2
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 2
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattgttttttataaataaatttca-----attgtcatctaattgtggtcct----tttttaaattt-tagattttccaatat-ttcctgc-----agtttgttttgtttt--------
|| | ||| || || || || |||| |||||| || ||||||||||| |||||||| || || || ||||| || ||||||||||| ||||| || ||||||  |  || | |||| |  ||  ||| ||      |||| |  | |  ||  || |    | | ||||| | ||| || |      | ||||| |     |  || ||| || ||        
GGTAGGGTGAAGATAGCTGAGCATGCATTGACAGGACATAAGGTTGCTATCAAGATCCTCAATCGTCGCAAAATCAAGAACATGGAGATGGAGGAGAAAGgtacaagttttgttttgtgtatccattccaccttagttgtgacttcacggtactcttggaatatataaatatatagcttctttttcgtcttccttcctttgaacttatttggtctttgatgcag

upper sequence: GLYMA08G26180.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 2
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattgttt-tttataaataaatttcaattgtcatctaattgtggtccttttttaaattttagattttccaatatttcctgcagtttgttttgtttt---
|| ||||| |||||||||||||||| ||| ||||| || || ||||| |||||||| |||||||| || ||||||||||||||||||||||||||||||||| |   |   ||  ||  |     |  |    ||||  | | |    ||      |   ||| |    |||    ||  |  |   | |||||   || |   
GGTAAGGTTAAAATTGCAGAACATGCATTAACTGGACACAAAGTTGCTATCAAGATCCTTAACCGTCGGAAGATAAAGAACATGGAAATGGAAGAAAAAGgtatggttcacttgcttggatgatgaccttgtctgtc--ccagtaa--gttaacaatcgtattgtgtcattttgtgtagattgttatgattgttaaattgtcac

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|24206158|gb|BU965411.1|BU965411
EST:     CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAG                         TGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
genomic: CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattg ... catgttgcagTGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
EST: gi|18040286|gb|BM308580.1|BM308580
EST:     CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAG                         TGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
genomic: CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattg ... catgttgcagTGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
EST: gi|208079704|gb|GD873722.1|GD873722
EST:     CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAG                         TGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
genomic: CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattg ... catgttgcagTGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
EST: gi|192305535|gb|FG998319.1|FG998319
EST:     CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAG                         TGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
genomic: CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattg ... catgttgcagTGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
EST: gi|209726300|gb|BW659613.1|BW659613
EST:     CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAG                         TGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
genomic: CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattg ... catgttgcagTGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
EST: gi|207785838|gb|GD755235.1|GD755235
EST:     CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAG                         TGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC
genomic: CAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattg ... catgttgcagTGAGAAGAGAAATCAAAATTTTAAGATTATTCATGCATCCTCACATTATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAAGGTCAAAATTGCAGAACATGTATTGACTGGCCATAAGGTTGCGATCAAGATTCTTAACCGACGCAAGATAAAGAACATGGAAATGGAAGAAAAAGgtttatattgttttttataaataaatttcaattgtcatctaattgtggtccttttttaaattttagattttccaatatttcctgcagtttgttttgtttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA