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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagacttcaatttgtcttatatgcctttaattaaagtgtggatttcacagtttcgagtgcacatgcttagttacttaaataatatgctttgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAACTGAGAAGTACACCTGCTATATCTCACCCAAAGTCATTGAAATTGCCAA

Basic information

species Glycine max
transcript GLYMA19G41120.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 3
-----------------gttagacttcaatttg-tcttatatgcctt-taattaa--agtgtggatttcacagtttcgagtgcacatgcttagttacttaaataatatgctttgatt-cacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAACTGAGAAGTACACCTGCTATATCTCACCCAAAGTCATTGAAATTGCCAA
                  |     |   ||| | ||||  ||   |  ||||| |  | |||  | |   |||||    |  ||     |||||| || |     | |  ||||  | |||||||||  ||||||| || ||||||||||||||||||||| | | |||||||  ||    ||   ||||  ||| |||| |||||  | || ||  | ||||
gtgagtctactggcaggatcttgttcatattagatctttcatttttcctaattgagcaatgtaaaatattcagttatagggccagcattttagttgctaagtcctttttttttggctgcacagGTTGGCCAATTTATGCACCTTCTTGGAGTCAAACCAACACTTCAGAAGGATTTGGAGGGTGTTCCTGTCATAACTCATCCAAAAACTTTAAAGCTTCCAA
















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|22524028|gb|BU082839.1|BU082839
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|7796797|gb|AW782191.1|AW782191
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|254322390|gb|GR837804.1|GR837804
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|298196328|gb|HO044719.1|HO044719
EST:     CCGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|208239211|gb|GE037205.1|GE037205
EST:     CAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTGCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|7925061|gb|AW831087.1|AW831087
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|11413286|gb|BF425297.1|BF425297
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCACCTTCTTGGAGTCAAACCAACGCCTAAGAAAGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|7591427|gb|AW707160.1|AW707160
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|192330291|gb|FK020576.1|FK020576
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|13480326|gb|BG509669.1|BG509669
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|192314667|gb|FK005949.1|FK005949
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|120493127|gb|EH221294.1|EH221294
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|6454707|gb|AW185390.1|AW185390
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|151407971|gb|EV277786.1|EV277786
EST:     CTGAGGTAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTAAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|9986531|gb|BE660639.1|BE660639
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|9986532|gb|BE660640.1|BE660640
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|19452880|gb|BM954290.1|BM954290
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|24136646|gb|BU927156.1|BU927156
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|19934893|gb|BQ079914.1|BQ079914
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|209724787|gb|BW672570.1|BW672570
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|22524928|gb|BU083739.1|BU083739
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|192314666|gb|FK005948.1|FK005948
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|6482896|gb|AW202106.1|AW202106
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|19452860|gb|BM954270.1|BM954270
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|7692565|gb|AW760668.1|AW760668
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|298174540|gb|HO017763.1|HO017763
EST:     CCGAGGCAGGATGGGAAGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTAAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|23733671|gb|BU765041.1|BU765041
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|21889139|gb|BQ742352.1|BQ742352
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|11688232|gb|BF595908.1|BF595908
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATNTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
EST: gi|24205547|gb|BU964800.1|BU964800
EST:     CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACA                         GTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA
genomic: CTGAGGCAGGATGGGAGGCTGCTATAAATCCTCATTTCTCCAATTATACAgttagacttc ... tgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacagtttcgagtgcacatgcttagttacttaaataatatgctttgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAACTGAGAAGTACACCTGCTATATCTCACCCAAAGTCATTGAAATTGCCAA
                                          ctttgat  putative branch site (score: 5)
                      ttagttacttaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagacttcaatttgtcttatatgcctttaattaaagtgtggatttcacagtttcgagtgcacatgcttagttacttaaataatatgctttgattcacagGTTGAACAATTTAAGCGCCTTCTTGGAGTCAAACCAACGCCTAAGAAGGAACTGAGAAGTACACCTGCTATATCTCACCCAAAGTCATTGAAATTGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT