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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtggatctacgttgtcttttgacatgtttatgtattcaatgttttacatgttagtgattatcaagatcagttgtgtgcttgaccattctgcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG

Basic information

species Glycine max
transcript GLYMA06G43930.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G43930.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G23280.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtactgtggatctacgttgtcttttgacatgtttatgtattcaatgttttac--atgttagtg----attatcaagatcagttgtg-tgcttgaccattctgcat-tggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG
  |  ||   ||| ||      |  || |  | ||||    |    |   |||   |||| | ||    || |||  |    ||| |  |  ||  |  |  | | | ||||||||||| ||||||||  |  |    || ||| | || ||| |  |||| |||||||| |||||| | || |||||||||||||||||| |||| |||||
gtgagcttgagatttattgccacagtttatttctttactcttcttcttcattagcaatgtcaatgtcttatgatctgggagggttttaattattttctttcttacgtgtggcagTTGTACTGGCCCAAGTTGTTGCAGCATAAGGTTAAACAAAGACTGACTAAAATGACTCAGATGCGTATTCGTATGAGGAAACTTGCTCTGAAAACAAG
















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|193552745|gb|FK506996.1|FK506996
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|193623854|gb|FK575582.1|FK575582
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|193675302|gb|FK618658.1|FK618658
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTTGACCAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTT-GACCAA
EST: gi|193636957|gb|FK578982.1|FK578982
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTACTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|254345742|gb|GR859389.1|GR859389
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|21889376|gb|BQ742589.1|BQ742589
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|18690832|gb|BM519680.1|BM519680
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|208070582|gb|GD867563.1|GD867563
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|6502229|gb|AW203602.1|AW203602
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|208163411|gb|GD959789.1|GD959789
EST:     AGTAGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACACATG                         TTGTATTGGCCCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAA
EST: gi|193639236|gb|FK586457.1|FK586457
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAA
EST: gi|193488212|gb|FK457953.1|FK457953
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTGGCCCAAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATTGGCCCAAA
EST: gi|208050265|gb|GD845488.1|GD845488
EST:     AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATG                         TTGTATTTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAA
genomic: AGTTGCCAAGGAATTATGAGAAGGCACTTGAAATCATAGACAAACATATGgtactgtgga ... gcattggcagTTGTATT-GGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatgttagtgattatcaagatcagttgtgtgcttgaccattctgcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG
                                gcttgac  putative branch site (score: 4)
            attatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgtggatctacgttgtcttttgacatgtttatgtattcaatgttttacatgttagtgattatcaagatcagttgtgtgcttgaccattctgcattggcagTTGTATTGGCCCAAACTTCTTATACACAAGATAAAGCAACGCTTGACCAAAATGACACAGATGAGGATACGTATGAGGAAACTTGCTTTGAAGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA