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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtgagtgtgaattttgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC

Basic information

species Glycine max
transcript GLYMA11G11310.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 3
aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtg----agtgtgaattttgt---tttaatgtt---gttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
              || | || ||||  | | | |   ||   |    |||||   | ||||| |  | ||    || ||   |||| |   |  |||||    || ||||||||| || ||||| || ||||| |||||||||||||| ||||| ||||||||||| || ||||| || || || || || || || || || ||||||
------------gtacgt-acctgcagctactaaagccactgaagt--ctgaatgtactcattagtatctgttttagcgtctgttttatgtgtacaatgtgtgagtgcagCAACATCTACTACATCAACGACAAGCTGGACAAGAGGACGTGGACCTACATCTTCGGCGCGTGCTGCGCGACGACGGTGTTCATCCCGTCGTTCCACAAC

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 3
aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtgagtgtgaattttgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
             ||  |  | ||| ||  |  |   |   |     || |    || |   ||  | || || ||  || |     || |      ||||||||| || ||||| || ||||| ||||||||| |||| ||||| ||||||||||| || ||||| ||||| || || || || || || || ||||||
-----------gtaaggttgcttgcttgctcgctcgca---tggttcgccggc-taactgtgtgccgcgtaagcgtacatata----tactaccaaacagCAACATCTACTACATCAACGACAAGCTGGACAAGCGGACGTGGACGTACATCTTCGGCGCCTGCTGCGCCACGACGGTGTTCATCCCGTCGTTCCACAAC

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 3
aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtgagtg--tgaattttgttttaatgt--tgtt-cagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
                       | |  |   |||  ||   |  || | | || |    | |   |    ||||  | |||  |   | |||||  |||| |||||||||||||||||||||||| || |||||||||||||| ||||| ||||| || ||||| || ||||| ||||| ||||||||||||||||| ||||||
-----------------------gtactttatataccaattctttcttcaggaaaatgagactaatgatgtagtggtttaatggtaagtgaatgtgttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACATACATATTTGGAGCATGTTGTGCAACCACAGTCTTTATTCCTTCCTTCCACAAC

upper sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtgag------tgtgaattttgttttaatgtt-gtt-cagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
                                                                    |   |     |    | ||    ||| | |    || |||      |||||  |    | | ||||      | || |  | |   |   ||| ||| |||||||||||||||||||||||| || |||||||||||||| |||||||||||||||||||| |||||||||||||| |||||||||||||| || ||||||
gcatctccctctctccctccctatcctcctcctactactactctctctctctctctctctctttctctgtctcttgttttttcttcacccaccacatttttttttcctttctttacaataaacaaagatctgaggcattttctgcaactgggcatgtcgtttgttgcagCAACATATATTACATAAATGATAATCTGGACAAGAGGACATGGACTTACATCTTCGGAGCCTGCTGTGCCACCACAGTCTTTATTCCTTCATTCCACAAC

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|24206334|gb|BU965587.1|BU965587
EST:     TGCACATTTCTTCTGTTTGGATCTGTTATACAATTGATAGCTTGTGCAAG                         CAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACAT
genomic: TGCACATTTCTTCTGTTTGGATCTGTTATACAATTGATAGCTTGTGCAAGgtacctactc ... tgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACAT
EST: gi|209726328|gb|BW659628.1|BW659628
EST:     TGCACATTTCTTCTGTTTGGATCTGTTATACAATTGATAGCTTGTGCAAG                         CAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACAT
genomic: TGCACATTTCTTCTGTTTGGATCTGTTATACAATTGATAGCTTGTGCAAGgtacctactc ... tgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACAT
EST: gi|298180126|gb|HO025341.1|HO025341
EST:     TGCACATTTCTTCTGTTTGGATCTGTTATACAACTGATAGCTTGTGCAAG                         CAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACAT
genomic: TGCACATTTCTTCTGTTTGGATCTGTTATACAATTGATAGCTTGTGCAAGgtacctactc ... tgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctgaaacaattcattggggtgtgagtgtgaattttgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC
                                       ttttaat  putative branch site (score: 3)
                                aattttgttttaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagacaaggaaccaacatcacatgcatgtcccataataaccttacctgctgaaacaattcattggggtgtgagtgtgaattttgttttaatgttgttcagCAACATATATTACATAAATGACAACCTGGACAAGAGGACTTGGACTTACATCTTCGGAGCTTGCTGTGCCACCACTGTCTTTATTCCTTCCTTTCACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
aagacaag
- - - - - -ccaacat
- - - - - - - - - - - - catgtcc
- - - - - - - - - - - - - - - - - - - -ccttacc
- - - - - - - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - caattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtgtga