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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgagtaaaaataaaaatccaaagaacagtaaaagagtgataaatgtgacaatctgaataaacataaaagcaagtcttatgttggccccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACTGTTGCAGTAGTTGATCTTGGAGGTGGATCTGTTCAAATGGCTTATGCAG

Basic information

species Glycine max
transcript GLYMA16G04770.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04770.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0094g01630.t01 (Vitis vinifera), 3'ss of exon 4
tttctgagtaaaaataaaaatccaaagaacagtaaaagagtg-ataaatgtgacaat-ctgaataaacataaaagcaagtcttatgttggcccca--catgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACTGTTGCAGTAGTTGATCTTGGAGGTGGATCTGTTCAAATGGCTTATGCAG
         |  |  |  | | |||   ||| |  ||      | | |  |   ||  |  ||||||   | || |  |||| |  ||| | |      | ||||| || || ||||||||| | || || ||||||| | | || ||  | || |||| ||| ||||||||||||||||| |||||||||||||| |||||  
----cccacattaccaccactgcaacacacatttcaaacccatacacacatacaaacacaaaataaaagaagaatcttgtctgaaattgcctcttattgtacagGTGACCATAAACTATCTATTAGGGAATTTGGGAAGGAAATACTCTCATACAGTTGGAGTGGTTGATCTTGGAGGTGGTTCTGTTCAAATGGCATATGCCA
















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|151410629|gb|EV280444.1|EV280444
EST:     GTTGAGTGGAAACCAAGAATGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCA
genomic: GTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCA
EST: gi|26057562|gb|CA800476.1|CA800476
EST:     CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|9902312|gb|BE611280.1|BE611280
EST:     CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|151404717|gb|EV274531.1|EV274531
EST:     GCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTGCTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|4293036|gb|AI441990.1|AI441990
EST:     CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|23732353|gb|BU764336.1|BU764336
EST:     CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|151409575|gb|EV279383.1|EV279383
EST:     CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|13181122|gb|BG352462.1|BG352462
EST:     CCGAT-CAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CCGATGCAGTTTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
EST: gi|5508917|gb|AI855475.1|AI855475
EST:     CGATGCAGTCTT-AGCGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGG                         GTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT
genomic: CGATGCAGT-TTCAGTGTTGAGTGGAAACCAAGAAGGAGCTTATCAATGGgtatgaatgt ... ccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtgacaatctgaataaacataaaagcaagtcttatgttggccccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACTGTTGCAGTAGTTGATCTTGGAGGTGGATCTGTTCAAATGGCTTATGCAG
            tgaataaacataaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgagtaaaaataaaaatccaaagaacagtaaaagagtgataaatgtgacaatctgaataaacataaaagcaagtcttatgttggccccacatgcagGTAACAATTAACTATCTACTGGGAAACTTGGGAAAGCATTATTCAGAAACTGTTGCAGTAGTTGATCTTGGAGGTGGATCTGTTCAAATGGCTTATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA