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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcttaatttgtgttttgctttagataaatgaatgagtggatgcgtttgtgtatagtgtacttgttttacactcaagttttactcaatgtatgggtgttagattgcaagaacattaatacagaattgcagatttatttcttttaaataatttcataggtcagagttgctttaatttcaaaaacaacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTCCCATTGTTTGTGTCTCCTGGAGTTCTGCAAAAGGAGAAGGACCACGTTG

Basic information

species Glycine max
transcript GLYMA03G38340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G62120.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtttcttaatttgtgttttgctttagataaatgaatgagtggatgcgtttgtgtatagtgtacttgttttacactcaagttttac--tcaatgtatgggtgttagattgcaagaacattaatacagaattgcagatttatttcttttaaataatttcataggtcagagttgctttaatttcaaaaacaacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTCCCATTGTTTGTGTCTCCTGGAGTTCTGCAAAAGGAGAAGGACCACGTTG
                                                                                 ||| | |   |   | ||| |   || || |  ||  ||||| ||  | | |    || | |  | | | |||| ||    | | |   | | | |||   | || | |             || || ||| | ||||| |||||||||||  ||||||| ||||| |||||  ||||||| |||||||| ||  |  ||||||||||||||||| | |
------------------------------------------------------------------------------gtgagtatcatcgtttctttattgtgatttgagt-taatcacattgattgaaagt---ggaatcaagtgtgtgaaatgatcattttgttttcattggtttt---tccatagATT-----------TTCTTTGATGCGGAAATCAAGAAAATGAAGGTCAAGAATTGCTATTTCCCTCTGTTTGTATCTCCTGGTGTCTTAGAAAAGGAGAAGGACCACATCG

upper sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtttcttaatttgtgttttgctttagataaatgaatgagtggatgcgtttgtgtatagtgtacttgttttacactcaagttttactcaatgtatgggtgttagattgcaagaacattaatacagaattgcagatttatttcttttaaataatt--tcataggtcagagttgctttaatttcaaaaacaacg---tgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTCCCATTGTTTGTGTCTCCTGGAGTTCTGCAAAAGGAGAAGGACCACGTTG
                                                                                                 | | ||||    ||  |    |||  | |     |   | |||  || |  || |   |   | | |  | |   |||||  | ||| ||  | |  |   |||||   || || ||| | || || ||||| |||||||||||||| |||||||||||  | ||||| || ||||| ||| | |||||||||||||| ||| |||
-------------------------------------------------------------------------------------------------tagttgttg--ctgtta----attcctccctttctattgtttttcttttcctagactttgaataagatattattattgctaaattttgaatgatattgaaatgcagACTTTCTTTGATGCGGAGATTAAGAAGATGAAAATCAAGAATTGCTACTTCCCTCTCTTTGTATCACCTGGTGTTTTACAAAAGGAGAAGGATCACATTG
















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|213588977|gb|DB971514.1|DB971514
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|213610669|gb|DB961144.1|DB961144
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|209724628|gb|BW677721.1|BW677721
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|193328627|gb|FK294003.1|FK294003
EST:     TTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: -TTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|192304983|gb|FG996115.1|FG996115
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATGTGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|208234905|gb|GE029188.1|GE029188
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAG
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAG
EST: gi|192330459|gb|FK022646.1|FK022646
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGGGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|207840337|gb|GD811356.1|GD811356
EST:     TATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: TATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
EST: gi|193672000|gb|FK616298.1|FK616298
EST:     GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAA                         GAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC
genomic: GTTGCTATATTCTGAGGCCTTGGTCAATGGCAATATGGGAGATCATGCAAgtgagtttct ... caacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttaaataatttcataggtcagagttgctttaatttcaaaaacaacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTCCCATTGTTTGTGTCTCCTGGAGTTCTGCAAAAGGAGAAGGACCACGTTG
                              ctttaat  putative branch site (score: 4)
                               tttaatttcaaaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcttaatttgtgttttgctttagataaatgaatgagtggatgcgtttgtgtatagtgtacttgttttacactcaagttttactcaatgtatgggtgttagattgcaagaacattaatacagaattgcagatttatttcttttaaataatttcataggtcagagttgctttaatttcaaaaacaacgtgcagGAGTTTTTCGATCCAGAAATAAAGAAAATGAAAATCAAGAACTGCTACTTCCCATTGTTTGTGTCTCCTGGAGTTCTGCAAAAGGAGAAGGACCACGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA