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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctgctgcatctttagtatgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgtacataattaactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT

Basic information

species Glycine max
transcript GLYMA11G12570.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G478876_T01 (Zea mays), 3'ss of exon 1
---atgctgctgcatctttagt--atgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgtacataattaact--agGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT
   |     |   |  |  | |  |   |   |    ||  ||  ||   |  ||| |  || ||  | |      ||||   |||   || ||||| |   |  |||||||| || |||||||| || ||||||||||||||||| || || ||||| ||||| ||| |  | ||  || |  | || || || ||||||||  ||
aacaaaacacgagagataaaatggacagtggctacaagtgtaatgttctggcgatagcttca-ctagtcgg-----catgttgattga-gtccataacttgttttagGGGTCAGGCCGAGAAGGAATTCAAGGTGGAGGTTGAAGCCATCGGCAAAGTGAGGCACAAGCACCTTGTCGGTCTCATCGGGTACTGCGCAGAAGGCCCT

upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G34500.1 (Arabidopsis thaliana), 3'ss of exon 1
atgctgctgcatctttagtatgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgta---cataatt--aactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT
   || ||   |   |  |||  || | |  | |||| |  || ||| | ||    || | |   |  | ||      || || |||    ||||||  |   |||||||| || ||||||||||| || || || || ||||| ||||| |||||||| |||||||| |||||| || || | ||||||||||| ||  |||||
---cttcttgtttactcttatattattgttttataaa-cagttttgt-agattttgatataagaaatgaatctgctaaatgatggtaaaatataattctattcagGGGTCAGGCGGAGAAGGAGTTCAAAGTTGAAGTAGAAGCAATTGGGAAAGTAAGACATAAGAACTTGGTTGGTCTGATGGGATATTGTGCTGACAGTGCT

upper sequence: GLYMA11G12570.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0063g02510.t01 (Vitis vinifera), 3'ss of exon 1
----atgctgctgcatctttagtatgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgtacataattaactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT
    |   |   | ||       ||  | |||||   |||     || |  |  |       ||   || ||||||||  | ||  ||||   |  ||   ||| || || ||  ||| |||||| |||||||| |||||||| |||||||||||||| |||||||| |||||  |  | || || ||||||||||||||| | 
gagcaatttttggaatgcaattcatatttatttatattaactttcttttacctaaaaaattcctggatgtaaattcatctg-atatttgt-tttgtttg--tagAGGGCAGGCACAGAGGGAGTTCAAGGTGGAAGTTGAAGCCATTGGAAAAGTAAGACATAAGAACTTGGTAGGCCTAGTTGGGTATTGTGCAGAAGGTCCC

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|298173298|gb|HO016634.1|HO016634
EST:     GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAA                         GGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGT
genomic: GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAAgtatgtcaca ... aattaactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGT
EST: gi|18039745|gb|BM308039.1|BM308039
EST:     GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAA                         GGGTCAAGCTGAGAAGGAGTTTAA
genomic: GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAAgtatgtcaca ... aattaactagGGGTCAAGCTGAGAAGGAGTTTAA
EST: gi|18730364|gb|BM525836.1|BM525836
EST:     GTTCTGCACGATGCTTTCGTCGTGGCTGTCAAGAATCTTCTCAACAACAA                         AGGTCAAGCTGAGAAGGAGTTTAA
genomic: GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAAgtatgtcaca ... aattaactagGGGTCAAGCTGAGAAGGAGTTTAA
EST: gi|192328153|gb|FK020414.1|FK020414
EST:     GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAA                         A
genomic: GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAAgtatgtcaca ... aattaactag-
EST: gi|192328153|gb|FK020414.1|FK020414
EST:     GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAA                         A
genomic: GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAAgtatgtcaca ... aattaactag-
EST: gi|298172943|gb|HO019927.1|HO019927
EST:     GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAA                         GGGTCAAGCTGAGAAGGAGTTTAAGGTGG
genomic: GTTCTGCACGATGCTTCCGTCGTGGCTGTCAAGAATCTTCTCAACAACAAgtatgtcaca ... aattaactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatatccccatcttattgaaaattcatgcgcattattgtacataattaactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT
                                 attattgtacataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctgctgcatctttagtatgctaatttagtgtaaaacctttctgtcatatccccatcttattgaaaattcatgcgcattattgtacataattaactagGGGTCAAGCTGAGAAGGAGTTTAAGGTGGAGGTTGAAGCTATTGGAAAAGTAAGGCATAAGAATTTGGTTCGTTTGGTAGGATATTGTGCAGAAGGTGCT

- -ctgctgc
- - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - gtaaaac
- - - - - - - - - - - - - - - - - - - - -ttctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcgc