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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttcttctgcacctagttctctgttttgatgattgaatacgctatcaaatatgaaattagcaaggattttttgttggttgttacctttgcaatt...

Basic information

species Glycine max
transcript GLYMA12G00600.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00600.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 5'ss of exon 4
ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttcttctgcacctagttctctgttttgatga---------------ttgaat---acgctatcaaata-tgaaattagca--------aggattttttgttggttgttacctttgcaatt---------------------------------------------------
| |||||||||||| || | ||||||||| || ||||| ||||||||||| ||||| ||  ||||||||||| | |||||||| | |||||| | || ||         || ||    |   | |               | |  |   | |   ||||||| ||  | ||| |        |  ||| | ||    | |||    ||    ||                                                   
AGTTCAGCAAATCTGAAACTATATTATGCTACATGTTTCTCTCTTATTGCTGGGATCATCATTTTTGGTGGTTTACTTGCACCAACTgtaagttatcatccaatttggattatcataatcagtaacgcttcttacttttttcgggttggatgtcttcaaataatgggaatagaatctggaaaaaaattctatgaaattagttttggttcttgttgagacataaacataaatcccagtttgtaaacatttttctttcttatctcag
















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|120491443|gb|EH219610.1|EH219610
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGGCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTACGGGGCACATCTTATGCAGATGTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|7924908|gb|AW830934.1|AW830934
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|19269603|gb|BM885859.1|BM885859
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|33389909|gb|CA853116.1|CA853116
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|298167160|gb|HO010599.1|HO010599
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCA
EST: gi|13480083|gb|BG509426.1|BG509426
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGAT
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGAT
EST: gi|192307758|gb|FK001702.1|FK001702
EST:     TTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|22525484|gb|BU084295.1|BU084295
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|33389270|gb|CA852477.1|CA852477
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|193623839|gb|FK575133.1|FK575133
EST:     TAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACGTAGGGGGCACATCTTATGCAGTATTTTATTG
genomic: TAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGAC-TAGGGGGCACATCTTATGCAG-ATTTTATTG
EST: gi|120491318|gb|EH219485.1|EH219485
EST:     TTTCTGTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
EST: gi|12689436|gb|BG155833.1|BG155833
EST:     TTTCTCTTATTGCCGGGATAATTCTTTNTG-TGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACT
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACT
EST: gi|192307757|gb|FK001701.1|FK001701
EST:     TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT                         TTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA
genomic: TTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttc ... aatttctcagTTGGAGCTTAAGCTTGGACTAGGGGGCACATCTTATGCAGATTTTATTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGTgtaagatttcttctgcacctagttctctgttttgatgattgaatacgctatcaaatatgaaattagcaaggattttttgttggttgttacctttgcaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG