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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

Basic information

species Glycine max
transcript GLYMA20G24070.2
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|209718151|gb|BW677422.1|BW677422
EST:     GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG                         GTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
genomic: GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAGgtacaaattc ... ttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
EST: gi|209701922|gb|BW664576.1|BW664576
EST:     GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAG                         GTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
genomic: GCACATCTGGGATCGACAATAAGTTTACAACTGTGCAATTTACTGGAGAGgtacaaattc ... ttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGT
EST: gi|209698692|gb|BW656517.1|BW656517
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


 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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttctttgaatttcttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

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