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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcgcattttgcatagtttttttttttgtgtcgtgtgtgtgtttttgtgtggttaagattgaataaatattaagctgcatgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATC

Basic information

species Glycine max
transcript GLYMA04G03080.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03080.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g56820.1 (Oryza sativa), 3'ss of exon 4
----gt-atgttcgcattttgcatagtttttttttttgtgtcgtgtgtgtgtttttgtgtggttaagattgaataaata--ttaagctgcatgt-tgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATC
|| | | | || || || | || | ||| | | ||| | || ||| | |||| | || || | | || | | |||||||||||||||| || |||||| | ||||| ||||| || || ||||||||||| || ||| |||||| |||| | ||||||||||| |||||||
tatggtgacatactttttgtgtattgaacttatgattggctgctttgtaatgctatgcttggaatactatgaaaagttaacttttgttttatatgtatagGACTTTATGGCCCTCCTAGCTTATGAAGAGCCTGAGAAGTCACCTATGTTTCATCTACTAAGCCCAGAGTACAGGCAGAATGTTGCAGATAGCTTGAATC

upper sequence: GLYMA04G03080.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085602_T03 (Zea mays), 3'ss of exon 4
--------------------------------------------------------gtatgttcgcattttgca----tagtttttttttttgtgtcgtgtgtgtgtttttgtgtggttaagattgaataaatattaagctgcatgt--------tgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATC
||| || ||| || | | || || |||| | ||| | || | |||| | ||| | ||||||| | || | | |||||||||||||||| || |||||| | ||||| ||||| || || ||||||||||| || ||| |||| | |||| | |||||||| | |||||||
gtactttttccttgagcctacatgtctcaggaccattctgacagctaaaataatttttattttaacatagaacaccaatggattgattacttgttccagatgtttaattgc-tactgttattacagaa-agatattaaaatacaacttttgattgtatagGACTTTATGGCCCTCCTGGCTTATGAAGAGCCGGAGAAGTCACCTATGTTTCATCTACTAAGCCCAGAGCACAGGCAGAATGTTGCAGAGGGCTTGAATC

upper sequence: GLYMA04G03080.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g13280.t01 (Vitis vinifera), 3'ss of exon 4
gtatgttcgcattttgcatagtttttttttt-tgtgtcgtgtgtgtgtttttgtg--tggttaagattgaataaatattaagctgcatgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATC
|||||| | | | | || | || | | |||||| | | | | | || | | ||| ||| | || |||||||||| ||| | || || |||||| |||||||||| |||||||||||||||||||| || ||| | || |||||||| || |||||||||||||||||
gtatgtctttttctgaggcaaaccatcttaaacatttctactcaattattttgttcttcatcagaactaaagacaaatt--gct-cctgctgcagGACTTCATGACTCTGCTAGCTTATGAGGAGCCAGAAAAATCCCCAATGTTTCATCTGCTAAGCCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACA

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|208198919|gb|GD997256.1|GD997256
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAA-GCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|15287071|gb|BI470962.1|BI470962
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|192298544|gb|FG989220.1|FG989220
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|19054068|gb|BM732735.1|BM732735
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAANGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|9566116|gb|BE475554.1|BE475554
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCANATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCA
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCA
EST: gi|298168072|gb|HO013335.1|HO013335
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAG
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAG
EST: gi|209723413|gb|BW679947.1|BW679947
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|254325123|gb|GR834548.1|GR834548
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|27808942|gb|CB063364.1|CB063364
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
EST: gi|13788314|gb|BG650906.1|BG650906
EST:     CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAA                         GACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT
genomic: CCAAATTGGGCCCTTTCGGAAAGGAGCCCAAATATATGGAAAAGCTTGAAgtatgttcgc ... catgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgtgtttttgtgtggttaagattgaataaatattaagctgcatgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATC
                    ttaagattgaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcgcattttgcatagtttttttttttgtgtcgtgtgtgtgtttttgtgtggttaagattgaataaatattaagctgcatgttgcagGACTTTATGGCCCTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT