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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagatgcatcacttcttttaacattatttagttccaaaccactacttgcttgatgtaaataacttgaatttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG

Basic information

species Glycine max
transcript GLYMA14G37520.1
intron # 31
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 31
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 19
---------------gtagatgcatcacttctt--ttaacattatttagttc-caaaccactact-tgcttgatgtaaataacttgaatttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG
               ||  |   ||||| |        | ||||  || ||| |  |     ||| |  | | || |  | |  |  |   |      |  | ||| |||||||||||||||||||||||||| || || || || || |||||||| ||||||||||||
gttaattcaggctatgtgaaattatcacatgcagacatatattacgtaattcacctattgtaactattatcggtgcactttatctttacagtcttctctgtt-cagATTAGAACCTGTAATTATTGAGCTTGAACGGCAGCGTGCTCCAGTTGTTGTCATATCTCACCAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 31
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 20
gtagatgcatcacttcttttaacattatttagttccaaaccactacttg--cttgatgtaaataacttgaatttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG
     |   |   |   ||  || |  ||       ||  ||  |  |   | | | | ||||| |   | |||      | |||||||| | |||||||| || |||||| | || |||||| |||| ||||| || |||||||||||||||
----gtatgttcttctcttctacttctttctacgtgaagtcataaactaaacctcaggaaaatatcgctacttt-----gacaatgcagGCTTGAACCTGTGATCATTGAGTTAGAACGACAAAGAGCTCCTGTCGTCGTGATATCTCACCAG

upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 31
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 20
gtagatgcatcacttcttttaacattatttagttccaaaccac-tacttgcttgatgtaaataacttgaat----ttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG
||          ||  |   || | |  || ||   ||   |  || ||  |  |  | | | | | ||||    |||    | ||||||||| | || |||||||| ||||||||||| || ||||||||||||||||| |||||||||||||||
gtttgcaatctgctgttacaaagaatgatttgtcaaaacttaaatattttttccaactgatttattagaataaactttctgcattaatgcagGCTGGAGCCTGTAATCATTGAGCTTGAACGGCAACGAGCACCTGTTGTAGTGATATCTCACCAG

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|8403732|gb|BE059428.1|BE059428
EST:     GTCTTACTTAGATGTTATTCAAAG                         GTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGT
genomic: GTCTTACTTAGATGTTATTCAAAGgtagatgcat ... aataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGT
EST: gi|213613561|gb|DB978638.1|DB978638
EST:     CTTAGGTATCGTTATCCTCGTGGAGAGTCTTACTTAGATGTTATTCAAAG                         GTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGT
genomic: CTTAGGTATCGTTATCCTCGTGGAGAGTCTTACTTAGATGTTATTCAAAGgtagatgcat ... aataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaaaccactacttgcttgatgtaaataacttgaatttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG
                  ttgatgtaaataactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagatgcatcacttcttttaacattatttagttccaaaccactacttgcttgatgtaaataacttgaatttttaataataatgcagGTTAGAACCTGTAATTATTGAGCTTGAGCGACAACGAGCACCTGTTGTTGTGATATCTCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT