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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcacttgctgcctctatataagcctaatctaccttaattttcattattatttttcaggagtttcttgtcttttagtcaaataaactccctgtaaagtagtcttatttgagtgccaaaatttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAAACCACTCTTGTTGCTCTTCAAGACATAATGCTGGATAAAGTTCTTGATG

Basic information

species Glycine max
transcript GLYMA08G13110.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 16
lower sequence: AT2G34710.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaaatcacttgctgcctctatataagcctaatctaccttaattttcattattatttttcaggagtttcttgtcttttagtcaaataaactccctgtaaagtagtcttatttgagtgccaaaatttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAAACCACTCTTGTTGCTCTTCAAGACATAATGCTGGATAAAGTTCTTGATG
                                       ||| |  ||    |     |   || |||  | | | | | |  || |   ||       ||  | || |  | | | |  |    | || |||| || || || ||||| || ||||||||| | ||  | |||||||| ||||| |||||||| || ||||||||||||||||| || ||    ||||| |
--------------------------------------gtaagtaacaaggcttcccattcaga-ttttgtatttgtgactagaacatgttctt----gagatgactgacataaattctca----tctgtagGCTTCACCGGTTTTCACATTCGCAAACCAAACCGGTTTAGACATGCTGGAAACGACTCTTGTAGCCCTTCAAGACATAATGCTAGACAAGACCCTTGACG

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaaatcacttgctgcctctatataagcctaatctaccttaattttcattattatttttcaggagtttcttgtcttttagtcaaataaactccctgtaaagtagtcttatttgagtgccaaaatttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAAACCACTCTTGTTGCTCTTCAAGACATAATGCTGGATAAAGTTCTTGATG
                                          |    ||| |  ||||| | ||| | ||     | ||||  | |        |    | | |||| |||  | |       | |   ||||| || || || ||||| |||||||||||||||||  | |||||||||||||| || ||||| || ||||| || |||||||| || |||   |||||||
-----------------------------------------gtaagaattctgtttttttaagaggtgctcaa--tctagttta-tggttcggtttgggaattgtctgatt--attttttggttct---cagGCCTCACCGGTATTCACATTTGCAAACCAAGCTGGTTTAGACATGCTTGAAACTACACTTGTGGCACTTCAGGATATAATGCTCGACAAAACACTTGATG

upper sequence: GLYMA08G13110.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv10s0003g04670.t01 (Vitis vinifera), 3'ss of exon 16
--------------------------------------------------------------------gtaaatcacttgctgcctcta--tataagcctaatctaccttaattttcattattatttttcaggagtttcttgtcttttagtcaaataaactccctgtaaagtagtcttatttgagtgccaaaatttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAAACCACTCTTGTTGCTCTTCAAGACATAATGCTGGATAAAGTTCTTGATG
                                                                      |  |   |||    || |   |||  |  |  | | |||   || |||  |  |       |   | | |||  ||||     || ||||    | | | ||  |    | ||| || | |     ||||||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||||||||||||||| || || |||||||| |||||||| || ||  |||||||||
gtaattgctcttatgtttgctccaaaattttccgcaacttttttacaacgaacatccaagtgaaaagcacagctttattgtgaactattcctatgtgttttcttttcctcccttctcaaaacaaccaaatggagctctgttggattttgcattaacaaacaaaat-tgatgtgattgactgtgattgactacga--atgcagGCATCTCCAGTTTTCACATTTGCTAACCAGGCTGGGCTTGATATGCTTGAAACCACTCTGGTGGCCCTTCAAGATATAATGCTAGACAAGATTCTTGATG

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|19938252|gb|BQ081634.1|BQ081634
EST:     AACTTTGGCACCATCCAGATGCAATATTGTGCTGTTCTGTAAAAACAAAT                         GCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAA
genomic: AACTTTGGCACCATCCAGATGCAATATTGTGCTGTTCTGTAAAAACAAATgtaaatcact ... atttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAA
EST: gi|9902811|gb|BE611779.1|BE611779
EST:     AACTTTGGCACCATCCAGATGCAATATTGTGCTGTTCTGTAAAAACAAAT                         GCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAA
genomic: AACTTTGGCACCATCCAGATGCAATATTGTGCTGTTCTGTAAAAACAAATgtaaatcact ... atttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAA
EST: gi|57574689|gb|CX547664.1|CX547664
EST:     AACTTTGGCACCATCCAGATGCAATATTGTGCTGTTCTGTAAAAACAAAT                         GCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAA
genomic: AACTTTGGCACCATCCAGATGCAATATTGTGCTGTTCTGTAAAAACAAATgtaaatcact ... atttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtcaaataaactccctgtaaagtagtcttatttgagtgccaaaatttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAAACCACTCTTGTTGCTCTTCAAGACATAATGCTGGATAAAGTTCTTGATG
                                          aaaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcacttgctgcctctatataagcctaatctaccttaattttcattattatttttcaggagtttcttgtcttttagtcaaataaactccctgtaaagtagtcttatttgagtgccaaaatttatgcagGCATCTCCAGTGTTCACCTTTGCAAACCAAGCTGGACTTGACATGCTTGAAACCACTCTTGTTGCTCTTCAAGACATAATGCTGGATAAAGTTCTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA