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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttctttcaatgcttttcctctatgagttgtattcatttattctaaatcttaaccttttgcatatatgactacag

Basic information

species Glycine max
transcript GLYMA12G15470.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G15470.2 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 5'ss of exon 5
ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttctt--tcaatgcttttcctctatgagttgtattcatttatt-ctaaatcttaaccttttgcatatatgactacag
 | ||||||||  | || || || ||||| |  |  || || || ||||||||||||||||| |||||| |||||||| |  ||| |  |||     ||   |   |  |   |   | || |||  |   ||| |||   || | |  |  ||     
TTATTTAGGGGGCTTGCGTACATTCATACTGTTCCAGGGGTCTGTCATAGGGATGTGAAGCCACAAAATGTTTTGgtaggtattcatgatcagattattattttgctatgcgatggcctttgattattggctctgaactcctttcttgcaatacag---

upper sequence: GLYMA12G15470.2 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G045330_T02 (Zea mays), 5'ss of exon 5
ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttcttt---caatgcttt-tcctctatgagttgtattcatttattctaaatct-taaccttttgcatatatgac-tacag
 | ||||| ||  |||| ||||| ||||  | ||  ||||| |||||||||||||||||||| |||||  ||||||||||  |  | |   ||| | ||| | ||   |  | | |  | |||  |||| |||   |  | |  |   | | |||  |||||
CTTTTTAGAGGCCTAGCTTATATTCATAATGTACCAGGAGTCTGCCATAGGGATGTGAAGCCACAAAACGTTTTGgtatgtgtcatgtggacaaggatttgttcttcctttgatttggtaattagttctgaattggtctcgtcgtctctctttgatgtacag

upper sequence: GLYMA12G15470.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 5'ss of exon 5
ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgct-----ttcttt--caatgcttttcctcta-tgagttgtattca---------tttattctaaat--cttaaccttttgcat---atatgactacag
|| ||||||||  | || ||||| ||||| |  |  || |||||||||||||||||||||||||||||| || ||||||  |     || |||   || | || |    |  ||| |    | |          |||  | |||||  |||   || || | |   | || | | |||
ATTTTTAGGGGGCTGGCCTATATTCATACAGTGCCTGGGGTTTGCCATAGGGATGTGAAGCCTCAAAATGTTCTGgtatattgttcattttttgataaagattatggcatgctgaatcccctccccttcccccctttcctttaaatgacttggactgtttctttgaacataattgcag

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|208291209|gb|GE092863.1|GE092863
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|10237492|gb|BE806380.1|BE806380
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193547442|gb|FK501939.1|FK501939
EST:     GAGTTTGCCATAGGGATGTAAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: GAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193519296|gb|FK473171.1|FK473171
EST:     GAGTTTGCCATAGGGATGTAAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: GAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|208175296|gb|GD975963.1|GD975963
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|37994214|gb|CF805960.1|CF805960
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTNTGGGAGTGCCANA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|192301989|gb|FG995159.1|FG995159
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193431643|gb|FK395149.1|FK395149
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193309170|gb|FK273990.1|FK273990
EST:     CCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: CCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193514122|gb|FK466980.1|FK466980
EST:     ATACCGCCCTGCGAGTTTGCCATAGGGATGTAAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193345633|gb|FK313744.1|FK313744
EST:     CCTC-AAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: CCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|22525206|gb|BU084017.1|BU084017
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|208072046|gb|GD871504.1|GD871504
EST:     CCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCCCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: CCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|208294438|gb|GE091681.1|GE091681
EST:     TACCGCCCTGCGAGTTTGCCATAGGGATGTAAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: TACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|254341725|gb|GR852862.1|GR852862
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|19935688|gb|BQ080542.1|BQ080542
EST:     GGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: GGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
EST: gi|193588938|gb|FK540980.1|FK540980
EST:     ATACCGCACTGGGAGTTTGCCATAGGGATGTGGAGCCTCAAAATCTTTTG                         GTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA
genomic: ATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttc ... atgactacagGTTCATCCTCTTACTCACCAAGTTAAGCTATGTGATTTTGGGAGTGCCAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTTTAGGGGATTAGCATATATCCATACCGCACTGGGAGTTTGCCATAGGGATGTGAAGCCTCAAAATCTTTTGgtatgctttctttcaatgcttttcctctatgagttgtattcatttattctaaatcttaaccttttgcatatatgactacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC