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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

Basic information

species Glycine max
transcript GLYMA20G24070.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
---tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
    |  ||| | | ||| | |    | |  |||||  |   ||| |   ||   | |  |      |  || ||   |   | |  |  |  || || | ||||  | ||||||||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||||||||| ||||| ||||| || ||||| ||| 
tgaataatctataagtttttgtagtttatatcttttccttgtttgcatgtagc--actgaagtagcggcattgcttaatatgtgtggtaattctt-tctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
tttttctttgaattt---cttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
| |  |  ||  | |   |||||   ||||   || |||    ||      ||  |   |   | |||  ||    | | |    | || ||||| |  |||||| || ||||||||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| || || || |||||||| || ||| 
tctggcagtgggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtcttg--tttgattatgcagtacattgtgtttctt-acagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G094497_T01 (Zea mays), 3'ss of exon 5
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattc--caccttttgacttcctc--ttttcctctctttttgtttgtcc-acagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
       || |||||       || ||  |||  ||     | |  | |||||||    |  |     |||  |   || | |  || || ||||| |   |||||| || ||||||||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| || || || || || || || ||| 
-accaggttaaatttaacaatgatattgttttcttta----gtaccctgtttattgagaaattcccatcttgtttgattatacagtcattgtgtttcttttacagGTTTTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTGCCCGAAGCCTACT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
            ||  |||| |     | |||||  ||||  |  ||  | || |  ||         ||   ||||||  | |||||     |||| |||| || ||||||||||| ||  |||| |||||||| ||||| || |||||||| || || || ||||| || |||||||| || || |||||||| ||| 
----------gtttgtttttgctaccaagttttaaagtatcagtgtc--tataatatac---------tcacattttccaatgttttt-----tccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
tttttctttgaatttcttttacatgttacttttattgta---ttggaatcagtttattccaccttttgacttcctcttttcctctctttttg--tttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
      |      ||  | |   || ||  | || | |    |||  ||||  || || |    | |   |   || ||   || |||| |     | |  |||||| || ||||||||||||||| |||| |||||||| || || ||||||||||| || ||||| ||||||||||| || || || || || ||||||||| 
-----gtcaagcctttctgtgattgctatctctagtatcagtttgagatcaacttctttctttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 4
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtc-cacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
||  |    |||||  ||||   | |||| || | |    | |      || | |      ||||| |     |||   | |||| |  ||  |     ||||  | ||||| || |||||| |||||||||||||||| || || ||||||||||| ||||| ||||| || || || || ||| |  | || || ||||
ttcctgcccgaattg-ttttctgttttaccttaagtaatgttgttcgtcttcagtttttgatttgattaatgatttaaatttcttctctttcatggtttagGTACTCAAAACACCGGTCTCATTGGACATGCTTGGACGTATCTTCAATGGTTCTGGGAAACCCATTGACAACGGCCCTCCCATTCTTGCAGAAGCCTACC

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|209701922|gb|BW664576.1|BW664576
EST:     GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG                         GTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
genomic: GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAGgtacaaattc ... ttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
EST: gi|151411391|gb|EV281202.1|EV281202
EST:     GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG                         GTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
genomic: GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAGgtacaaattc ... ttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
EST: gi|209713872|gb|BW684065.1|BW684065
EST:     GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG                         GTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
genomic: GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAGgtacaaattc ... ttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
EST: gi|209698692|gb|BW656517.1|BW656517
EST:     GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG                         GTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
genomic: GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAGgtacaaattc ... ttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC
               ttttgac  putative branch site (score: 3)
        ttccaccttttgactt  CT-rich tract
                                      tttttgttt  TA-rich tract