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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgaggatcatgagttgcattttgttgtgcctgactagtgtgaagatatttttttcttctgtgaaatttggttgaatgtttgatatgtttgttttcttgtgatcttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGGGAAAATCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTT

Basic information

species Glycine max
transcript GLYMA12G30910.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgagtgaggatcatgagttgcattttgttgtgcctgactagtgtgaagatatttttttcttctgtgaaatttggttgaatgtttgatatgtttgttttcttgtgatcttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGGGAAAATCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTT
           | |     || | | ||  |    | | |   ||   || |   || |||| ||| || ||         ||  | | | | |||| | |||| |     || | ||| || ||||| || |||||||||||  |||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| || |||||||| || || ||
----------gtaaatttgtgtaatctggagctattcattgaagttttgaaaccgttctctt-tgtaaagtt---------gtgagctttatctgttgttttgttac----ttcttagGAAAGAGACGGCCTTGGAGAGCTTTTCTGTTGTATGGGCCTCCTGGAACAGGAAAATCGTATTTGGCTAAGGCTGTTGCCACTGAAGCTGACTCTACCTT

upper sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 1
gtgagtgaggatcatgagttgcattttgttgtgcctgactagtgtgaagatatttttttcttctgtgaaatttggttgaatgtttgatatgtttgttttcttgtgatcttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGGGAAAATCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTT
  ||  ||  |  | ||  || |||||  |||   |||  |||  |  |||  |            | | ||| |||  ||  |   | |  |  |  || |   | ||    |||||| || |||||||| ||||| |||||  |||| ||||| || || ||||| |||||||||||  |||||||||| |||||||| ||||| || || || ||
aagaaagaaaaaaaagaaatg-attttaatgt---tgagaagt-cgtggatgct------------ggattttagtttgattctatctgttctcatgctcctccca-ctccccttcagGAAAGAGACGACCATGGAGGGCTTTTCTGTTATATGGTCCACCAGGAACAGGAAAATCATACCTAGCCAAGGCTGTTGCAACCGAAGCAGATTCTACATT
















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|193312133|gb|FK275609.1|FK275609
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|193448870|gb|FK414225.1|FK414225
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|208290707|gb|GE084115.1|GE084115
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|21601249|gb|BQ611580.1|BQ611580
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|15204253|gb|BI427021.1|BI427021
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|207831213|gb|GD803017.1|GD803017
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|193682576|gb|FK621700.1|FK621700
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTAAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|207713731|gb|GD694846.1|GD694846
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTAAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|193302600|gb|FK266124.1|FK266124
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAA
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAA
EST: gi|254331392|gb|GR843404.1|GR843404
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|193671905|gb|FK616259.1|FK616259
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|208326860|gb|GE118988.1|GE118988
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
EST: gi|17519421|gb|BM188463.1|BM188463
EST:     CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTG                         GGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG
genomic: CTTGCAGGAGGCTGTGATTTTGCCTGTGAAGTTCCCTCAGTTCTTTACTGgtgagtgagg ... ttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaaatttggttgaatgtttgatatgtttgttttcttgtgatcttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGGGAAAATCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTT
                  gtttgat  putative branch site (score: 5)
                                           tcttattttc  putative PPT
                                          atcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgaggatcatgagttgcattttgttgtgcctgactagtgtgaagatatttttttcttctgtgaaatttggttgaatgtttgatatgtttgttttcttgtgatcttattttcagGGAAAAGACGACCCTGGAGAGCTTTCTTGTTGTATGGACCTCCTGGAACGGGAAAATCATATTTAGCCAAGGCAGTTGCAACAGAAGCTGAGTCCACGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA