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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattccaaatttgtgccttttcagtgaccaaatacttttagttaaactgaaggattaaaagaaattattaaattgatctcacttgagaatgttttgttggttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCGGGAGTAGCCAGGAGGCAGAGGAATTTGCCTGTACAAGGTACAAGGCTGA

Basic information

species Glycine max
transcript GLYMA19G33650.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G33650.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0104g00320.t01 (Vitis vinifera), 3'ss of exon 3
gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattccaaatttgtgccttttcagtgaccaaatacttttagttaaactgaaggattaaaagaaattattaaattgatctcacttgagaatgttttgttggttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCGGGAGTAGCCAGGAGGCAGAGGAATTTGCCTGTACAAGGTACAAGGCTGA
                                                   ||    |||||        | ||| |   |    |||   ||| | |   |||||           | || ||| |    |||||||   || | | || || |  ||||| |||||||  | |||||||||||||| || |||||||| |||||||| |||   ||  || ||||| | |||||||| |||||||| |||||||||||
---------------------------------------------------atcatcaatttaattgacataagtcataga----tttagattagattttgggatttttct--tccctgaatttgctgagtcttgaga---ttatatcgggtgtttccagGTTTTGAGATCTTAGCATTTCCATGCAATCAATTTCTGAAGCAAGAGCCTGGGTCGAGTGAGCAGGCACAAGAATTTGCATGTACAAGATACAAGGCTGA
















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|298171406|gb|HO016438.1|HO016438
EST:     TTCCAATTACACCCAGTTAACTGAGCCTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|9819421|gb|BE554934.1|BE554934
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|10709776|gb|BF009500.1|BF009500
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|13477752|gb|BG507504.1|BG507504
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298166996|gb|HO010435.1|HO010435
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|15663056|gb|BI700427.1|BI700427
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|9820763|gb|BE556273.1|BE556273
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|208167184|gb|GD963030.1|GD963030
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAA
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAA
EST: gi|19453002|gb|BM954412.1|BM954412
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298187303|gb|HO034452.1|HO034452
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298197094|gb|HO041837.1|HO041837
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298173934|gb|HO017270.1|HO017270
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298168059|gb|HO013322.1|HO013322
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATA-AA-GACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298194861|gb|HO043333.1|HO043333
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298192806|gb|HO033240.1|HO033240
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298184031|gb|HO029244.1|HO029244
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|151397536|gb|EV267409.1|EV267409
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|192319134|gb|FK009102.1|FK009102
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         ATCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298166854|gb|HO010293.1|HO010293
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298166545|gb|HO009984.1|HO009984
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298195273|gb|HO043801.1|HO043801
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
EST: gi|298183535|gb|HO028748.1|HO028748
EST:     TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAG                         GTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG
genomic: TTCCAATTACACCCAGTTAACTGAGCTTTACAGCAAATATAAAGACAGAGgtatggtttt ... ttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagaaattattaaattgatctcacttgagaatgttttgttggttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCGGGAGTAGCCAGGAGGCAGAGGAATTTGCCTGTACAAGGTACAAGGCTGA
      aaattattaaattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtttttttaggtttacagagcagttggtgcacttgcatgttattggattccaaatttgtgccttttcagtgaccaaatacttttagttaaactgaaggattaaaagaaattattaaattgatctcacttgagaatgttttgttggttgatctcagGTCTTGAGATACTGGCATTTCCATGCAACCAGTTTCTGAAACAAGAGCCCGGGAGTAGCCAGGAGGCAGAGGAATTTGCCTGTACAAGGTACAAGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA