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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCCTACACCGTGGGTGGTTGGTTCTCTTGTGCCTATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtctgctccttgtcttgttccttctagaggaagaggagaggtgacttggtgggatttggaaagagaagttttggtaatgtaaattgtaatgtgctttggtggaatggtgaacag

Basic information

species Glycine max
transcript GLYMA04G35730.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G35730.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv17s0000g08560.t01 (Vitis vinifera), 5'ss of exon 4
TTTCCTACACCGTGGGTGGTTGGTTCTCTTGTGCCTATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaaga---------tgtctgctccttgtct--tgttccttctagaggaagaggagaggtgacttggtgggatttggaaagagaagttttggtaatgta-aattg--taatgtgctttggtggaatggtgaacag-----------------------------
|||||||||   |||||| |    || ||| | ||||||||||||||||| || |||||||| |  || |||||||| |||||||||| |||         ||  |     || | |  | | | ||         ||    |  ||  ||| | |  ||  |  | ||||   ||  || |  | || |   | |  || ||   |   ||  |||  |                              
TTTCCTACAATCTGGGTGCTCTCCTCCCTTCTTCCTATTGTTGGTGGAGTGGCGCTGGCATCAGCCACTGAGGCCTCCTTCAATTGgtgagaaaataaatatgattatatgttatttattatccttttctataagggaatttacttgttttgtttgagttcagttacagaaaaattattagttcagaagtaattgaaatggttatcttagattctgacaaaataatctcatcattttgttcctaaatcag
















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|31469095|gb|CD411123.1|CD411123
EST:     ATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTG                         GGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
genomic: ATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtc ... tggtgaacagGGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
EST: gi|10256147|gb|BE823913.1|BE823913
EST:     GTTGCACTGGCATCTGNNACAGAGNNNNCTTTCAATTG                         GGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
genomic: GTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtc ... tggtgaacagGGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
EST: gi|7145742|gb|AW507664.1|AW507664
EST:     ATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTG                         GGCTGGATTTTGGAGT
genomic: ATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtc ... tggtgaacagGGCTGGATTTTGGAGT
EST: gi|207704437|gb|GD686652.1|GD686652
EST:     CACTGGCATCTGTTACAGAGGCCTCTTTCAATTG                         GGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
genomic: CACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtc ... tggtgaacagGGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
EST: gi|192301535|gb|FG998443.1|FG998443
EST:     ATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTG                         GGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
genomic: ATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtc ... tggtgaacagGGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
EST: gi|58016526|gb|CX703268.1|CX703268
EST:     TTGTTGGTGGAG-TGCCACTGGCATCTGTTACAGAGGCCTCTTTCAATTG                         GGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA
genomic: TTGTTGGTGGAGTTG-CACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtc ... tggtgaacagGGCTGGATTTTGGAGTGCAATGGCATCCAATGTGACAAATCAATCTCGTAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCCTACACCGTGGGTGGTTGGTTCTCTTGTGCCTATTGTTGGTGGAGTTGCACTGGCATCTGTTACAGAGGCCTCTTTCAATTGgtaagatgtctgctccttgtcttgttccttctagaggaagaggagaggtgacttggtgggatttggaaagagaagttttggtaatgtaaattgtaatgtgctttggtggaatggtgaacag

- - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - -  GTGGAG