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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataattgaaaagtggcttctgggatctacttctcagtcacttcttgcatgcttttcaatggactacaaccatataaggttgctgtttaaggggcagagaaacaaatattggctttgtcttttatgctcatcatcctgtagtgaatcttattcttgtttcaatgttcataatgtag

Basic information

species Glycine max
transcript GLYMA08G07960.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 5'ss of exon 3
GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataattgaaaagtggcttctgggatctacttctcagtcacttcttgcatgcttttcaatggactacaaccatataaggttgctgtttaaggggcagagaaacaaatattggctttgtcttttatgctcatcatcctgtagtgaatcttattcttgtttcaatgttcataatgtag
||||| |||||||| |||||||||||||| ||||||||||| || ||| || |  |||| |||||  | ||| ||||||| || ||    ||||   | | |         |||| |  ||| |    | |||| |  |       |  | || |||   ||      ||  |  | |   ||||| ||   ||      ||| ||  |   |                                                           
GAACTTTTTGAAGGATATTACTTCTGTCAAGCACAAAGAGAAGACTTCTTTAAGCGAGCCAAGCCTTACAAGAACCATCCTACCATTGCAAGgtgtgacatt---------gcttatccgatttctaacgcagtaaagtg------gaatctcgatg---tatctatgtactatctagtgttttaatggttggatggtttaat-ttaacacag-----------------------------------------------------------

upper sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 3
GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaa----taattgaaaagtggcttctgggatctacttctcagtcacttcttgcatgcttttcaatggactacaaccatataag-gttgctgtttaaggggcagagaaacaaatattggctttgtcttttatgctcatcatcctgtagtgaatcttattcttgtttcaatgttcataatgtag
||||| |||||||| |||||||||||||| ||||| || ||||||||| ||||  ||||||||||  | ||||  ||||| ||||| || |||||||      ||   |||  |||||||| |  |    | |||||  | ||      |  |  ||  || |||  ||  || |  |  ||  | |   |  || | | ||  | || |||  ||  |  |  ||   ||   |  |  |||  | |||||  ||||     ||      ||| ||
GAACTATTTGAAGGATATTACTTCTGTCAAGCACAGAGGGAGGATTTCTTTCAGCGAGCTAAGCCTTACAAGGGTCATCCTACAATTCTGAGgtaaatgtttcaacccaaacctggcttctagatt----tgctcagctagttggaatgtcatcctcc-tgtact--aattatcttcgtatttttatagcacaggaacaaaaggacatcttgaattcctactacatttacaatttaatcaagttgaacttatg-ttgtacatctgcatgctatgcag
















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|151410591|gb|EV280406.1|EV280406
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298199306|gb|HO042669.1|HO042669
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|24135848|gb|BU926358.1|BU926358
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298184831|gb|HO030044.1|HO030044
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|192328547|gb|FK023551.1|FK023551
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298167316|gb|HO010755.1|HO010755
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|254330221|gb|GR839774.1|GR839774
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298164922|gb|HO010919.1|HO010919
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298167948|gb|HO013211.1|HO013211
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|22541663|gb|BU091506.1|BU091506
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298178170|gb|HO023905.1|HO023905
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT
EST: gi|298187812|gb|HO031769.1|HO031769
EST:     GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAG                         GATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATACCAGTTAGCTTCTT
genomic: GATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataat ... cataatgtagGATGCAGAAACTTGCAAAAGAGTTAGGTGTAGTCATTCCAGTTAGCTTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACTCTTTGAAGGTTATTACTTCTGTCAGGCACAAAGAGAGGATTTCATTCAAAGAGCTAAGCCACATAAGGACCATCCCACAATCCTCAGgtaaaataattgaaaagtggcttctgggatctacttctcagtcacttcttgcatgcttttcaatggactacaaccatataaggttgctgtttaaggggcagagaaacaaatattggctttgtcttttatgctcatcatcctgtagtgaatcttattcttgtttcaatgttcataatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT