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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaccttgtttgcttattgtttatttaacctttgttgaattgttgaggaagaaaagttgatacctagctataatcatggtttgaaattgttgcaccgtgaaatccagtgatcttataccttacctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCACAGAAGTTTCTGAACTGTCATTTTTTCAGTACCTTTTTCTACAAGAGG

Basic information

species Glycine max
transcript GLYMA07G37640.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G37640.4 (Glycine max), 3'ss of exon 3
lower sequence: AT3G06910.1 (Arabidopsis thaliana), 3'ss of exon 3
gttaccttgtttgcttattgtttatttaacctttgttgaattgttgaggaagaaaagttgatacctagctataatcatggtttgaaattgttgcaccgtgaaatccagtgatcttataccttacctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCACAGAAGTTTCTGAACTGTCATTTTTTCAGTACCTTTTTCTACAAGAGG
||||           ||    | |  | |  | |  | |    ||||  |   ||  ||  |  |||  ||  | |    | |   |||        || ||| ||   ||  || |       || || |||| || ||| | ||  | | |||||||||||| |||||    ||||| ||| |||||||||| || ||||||||||||| ||| ||||||| ||  | |
gttagtcgacgcatctaaatctcacgtgatttcttcttagagattga--atataattttcttgtctaattaggacc----tctatgatt------tggtaaaaaccttggactttgt------tctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
















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|193564183|gb|FK516694.1|FK516694
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|207685555|gb|GD667669.1|GD667669
EST:     TTAGACCGGGTGCATGGTTAAATGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: TTAGACCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|208055169|gb|GD851156.1|GD851156
EST:     TGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: TGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|193459686|gb|FK423893.1|FK423893
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|208298330|gb|GE089723.1|GE089723
EST:     GACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: GACCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|193357955|gb|FK318967.1|FK318967
EST:     CCGGGTGCATTGGTTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CCGGGTGCAT-GGTT-AAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|208107846|gb|GD902022.1|GD902022
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|193719467|gb|FK651855.1|FK651855
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|193624423|gb|FK573435.1|FK573435
EST:     TGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGA
genomic: TGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGA
EST: gi|193651025|gb|FK597590.1|FK597590
EST:     TGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: TGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|193619692|gb|FK570860.1|FK570860
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|208178234|gb|GD975779.1|GD975779
EST:     GACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: GACCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
EST: gi|15662185|gb|BI699556.1|BI699556
EST:     CGGGAGAAAAGTTTCAATGCCTTAGACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA
genomic: CGGGAGAAAAGTTTCAATGCCTTAGACCGGGTGCATGGTTAAACGATGAGgttaccttgt ... acctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttgaaattgttgcaccgtgaaatccagtgatcttataccttacctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCACAGAAGTTTCTGAACTGTCATTTTTTCAGTACCTTTTTCTACAAGAGG
                                        accttac  putative branch site (score: 3)
                                         ccttaccttt  CT-rich tract
       aaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaccttgtttgcttattgtttatttaacctttgttgaattgttgaggaagaaaagttgatacctagctataatcatggtttgaaattgttgcaccgtgaaatccagtgatcttataccttacctttgcagGTAATAAATGTGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAGCCACAGAAGTTTCTGAACTGTCATTTTTTCAGTACCTTTTTCTACAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG