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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgcagaagaattattctttaactattttcttgttttctatgtgccttgagtatgcataatatatgtatgtatcttaaattttttccctttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAGAACTTTGAGATATTACTGTGTATTGGAAACAAAGTGGACCTGGTTCCTA

Basic information

species Glycine max
transcript GLYMA16G21560.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G21560.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g02260.t01 (Vitis vinifera), 3'ss of exon 3
---------------tgtgcagaagaattattctttaactattttcttgttttctatgtgccttgagtatgcataatatatgtatgtatcttaaattttttccctttatg--------tgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAGAACTTTGAGATATTACTGTGTATTGGAAACAAAGTGGACCTGGTTCCTA
               |        ||||| ||  | ||   ||   ||  ||| | || |   ||    |  ||||| | ||| ||  |  ||   | | | | | ||||        ||||||  || ||  | | |||||||| ||| ||||| |||| |||||||||||| || ||||| |||||| | ||| |||| ||||||||||| || |||||  
gttagccctatcctattgctttctgaattctttgtgaaagcttcaattagttt-tgtgggaactgccagtttataatttttgtgtggctgatacgctgtcttcttgtatggctctgcctgcagCTGTCATCTTTTGTTGCACTTCAAGATTGGGTTTCTCACACTGATATTCAAAATTTTGACATATTATTATGTGTTGGGAACAAAGTGGATCTTGTTCCAG
















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|208162697|gb|GD960531.1|GD960531
EST:     CCTGTTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCTG-TCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|192297628|gb|FG989921.1|FG989921
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|192333176|gb|FK026505.1|FK026505
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|207807353|gb|GD777044.1|GD777044
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|151405714|gb|EV275528.1|EV275528
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|298189562|gb|HO037965.1|HO037965
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|151409293|gb|EV279101.1|EV279101
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
EST: gi|209728151|gb|BW655386.1|BW655386
EST:     CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAA                         CCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG
genomic: CCCTGTCTCGACGAATGACTGCACTGGTGATGGTTTTTGACATGAATGAAgttagttcct ... ttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgagtatgcataatatatgtatgtatcttaaattttttccctttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAGAACTTTGAGATATTACTGTGTATTGGAAACAAAGTGGACCTGGTTCCTA
                                   ttttttccctttatgt  CT-rich tract
       tatgcataatatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgcagaagaattattctttaactattttcttgttttctatgtgccttgagtatgcataatatatgtatgtatcttaaattttttccctttatgtgcagCCATCTTCCCTAGCTGCACTTCGAGAATGGGTATCTCGCACTGATATTCAGAACTTTGAGATATTACTGTGTATTGGAAACAAAGTGGACCTGGTTCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
tgtgcag
- - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - -gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgt