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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTAATTTGCATTTTCGTGGGGCCCCAATAGAAGATCTCTGCTTGGACTTCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattcagtctgttttttttacctggtttttgttttggttctgattctgtctgtaataaaaattgctttgaacttactgtcaaactttcag

Basic information

species Glycine max
transcript GLYMA12G03640.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 11
lower sequence: AT4G38600.1 (Arabidopsis thaliana), 5'ss of exon 11
TGCTAATTTGCATTTTCGTGGGGCCCCAATAGAAGATCTCTGCTTGGACTTCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattcagtctgttttttttacctggtttttgttttggttctgattctgtctgtaataaaaattgctttgaacttactgtcaaactttcag
| || ||||   ||| |||||   || |||||||||||||| |||||| ||||| || ||||| ||||| ||||||||| ||| | | |||||||||||||||     | ||  |           ||   | || ||||      ||   ||||  |       ||||||    || | ||||     || |||
TTCTGATTTATGTTTACGTGGATGCCGAATAGAAGATCTCTCCTTGGAATTCACGCTACCTGGCTATCCTGAGTACATCCTGAGATCAGGAGATGAAATTgtactgtcttagcttacaccccacctcttactattctttta-----gaacatgtccat------gattgctgatgacgtgctgttttg-ttacag

upper sequence: GLYMA12G03640.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 5'ss of exon 11
TGCTAATTTGCATTTTCGTGGGGCCCCAATAGAAGATCTCTGCTTGGACTTCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgta---tgtattcagtct-----gtttttt------ttacctggtttttgttttggttctga-----ttctgtctgtaataaaaattgctttgaa-------cttactg--tcaaactttcag
|||||||||   ||| |||||||| |||||||||||||||||  |||| ||||| ||||||||||||||||| ||||| |||||||| ||||| |||| ||||   || || |  |||     |  | ||      ||   ||| |||| |||    | ||      || |||   |   ||| ||     ||||       || | |   | ||  ||||||
TGCTAATTTATGTTTCCGTGGGGCGCCAATAGAAGATCTCTGTCTGGATTTCACTCTTCCTGGTTATCCAGACTACATTTTGAAACCAGGAGAAGAAAATgtaatttgcataccctcttgaatgcctcttcaaaattttgatggattttttttcccctttggcatatttgtgttgtttgcaaagatgttcctgaaagatctcctcatttgtttaatttttcag
















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|208098256|gb|GD892241.1|GD892241
EST:     TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATT                         GTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
genomic: TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattc ... aaactttcagGTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
EST: gi|9259017|gb|BE347164.1|BE347164
EST:     TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATT                         GTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
genomic: TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattc ... aaactttcagGTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
EST: gi|15815265|gb|BI787540.1|BI787540
EST:     TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATT                         GTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
genomic: TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattc ... aaactttcagGTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
EST: gi|192301647|gb|FG997603.1|FG997603
EST:     TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATT                         GTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
genomic: TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattc ... aaactttcagGTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
EST: gi|192327460|gb|FK017817.1|FK017817
EST:     TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATT                         GTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
genomic: TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattc ... aaactttcagGTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
EST: gi|9899529|gb|BE608497.1|BE608497
EST:     TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAAATGAAATT                         GTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG
genomic: TCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattc ... aaactttcagGTTGACATCAATAATCTAGAGGAGTACATATCCATGGTGGTTGAGGCAACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTAATTTGCATTTTCGTGGGGCCCCAATAGAAGATCTCTGCTTGGACTTCACACTTCCTGGTTATCCAGAGTACATCTTGAAACCTGGAGATGAAATTgtatgtattcagtctgttttttttacctggtttttgttttggttctgattctgtctgtaataaaaattgctttgaacttactgtcaaactttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG