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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttttgtattttatccatagaaatgtaaaactctcaattatatcgtctgacaatattttatgtcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG

Basic information

species Glycine max
transcript GLYMA13G20790.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 5
gtactttttgtatttta--tccataga--aatgtaaaactctcaattat----atcgtctgacaatatt-ttatgtctt-ttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG
|||   ||||| | ||     || |||  | |||  |      || |      ||| ||| |   | || |||||| || || |||    || ||||| ||||  |||||||| |||||||| ||||| || || || ||||||||||||||||||| |
gtaacatttgtttcttcgtctcacagattattgtctagtatgaaaatgaggcaatcatcttatgctcttattatgttttgttccagTATGAATATTGGGGAGGATGGTATTGCCCTTGCTGAAGCTGTTCACGGCTCTGCACCTGATATTGCTGGAATG

upper sequence: GLYMA13G20790.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 5
gtactttt-tgtattttatccatagaaatgtaaaactctcaattatatcgtctgacaatattttatgtcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG
|||  ||  | |||| ||||      ||| || |    |||  || |||  || |||   ||     || |   ||||||||| ||||| |||||||||||||| |||||||| || || |||||||| ||||| |||||||||||||||
gtatcttcatttattctatcatctttaatttatatgattcatatagatc--ctcacatctttcggcttcctacacagCTGCAATATTGGAGAGGGAGGTATTGCTCTTGCTGAAGCCGTTCATGGTTCTGCACCAGATATTGCTGGAAAG
















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|209702313|gb|BW667501.1|BW667501
EST:     ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
genomic: ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
EST: gi|151406995|gb|EV276810.1|EV276810
EST:     ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCGAGGGAGGTACTGCACTTGCTGAGGCTGTACATGGTTC
genomic: ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
EST: gi|21677612|gb|BQ629963.1|BQ629963
EST:     ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
genomic: ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
EST: gi|254321137|gb|GR827586.1|GR827586
EST:     ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
genomic: ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
EST: gi|22930892|gb|BU548031.1|BU548031
EST:     ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
genomic: ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
EST: gi|213612273|gb|DB976850.1|DB976850
EST:     CTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCCAGGGAGGTATTGCACTTG-TGAAGGCTGTACATGTTT
genomic: CTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTG-AGGCTGTACATGGTT
EST: gi|7924579|gb|AW830605.1|AW830605
EST:     ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAG                         CTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC
genomic: ATTAGTGACCTTTGTGCTGGCTTGGTTGGGGGATTGGGTTTAACACCAAGgtactttttg ... tcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaaatgtaaaactctcaattatatcgtctgacaatattttatgtcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG
                           gtctgac  putative branch site (score: 3)
                                           tgtctttt  putative PPT
                                  aatattttatgtcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttttgtattttatccatagaaatgtaaaactctcaattatatcgtctgacaatattttatgtcttttgcagCTGCAACATTGGCGAGGGAGGTATTGCACTTGCTGAGGCTGTACATGGTTCGGCACCTGATATTGCTGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA