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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ggtaatcttcatttttatggatatttacctgcttcactctttctctggtttaattgttgaaagattgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAAT

Basic information

species Glycine max
transcript GLYMA18G08370.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------ggtaatcttcattttta---tggatatttacctgcttcactct---ttctctggttt---aattgttgaaagattgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAAT-
                                                 ||||||    |||    | |||||| ||||     || ||    |   ||  ||   | ||| || ||  || |||  ||||||||||||||| ||||| |||||||| || || |||||||||||  |||| ||||||||| 
gtacttgcttaatatcaagaacaagaaagctattacttccagcctgtcaaatcttttgctttgaatttgatattaacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttat--cagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG

upper sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 3'ss of exon 5
----------------------------------------------ggtaatcttcattttta---tggatatttacctgcttcactct---ttctctggttt---aattgttgaaagattgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAAT-
                                                 ||||||    |||    | |||||| ||||     || ||    |   ||  ||   | ||| || ||  || |||  ||||||||||||||| ||||| |||||||| || || |||||||||||  |||| ||||||||| 
gtacttgcttaatatcaagaacaagaaagctattacttccagcctatcaaatcttttgctttgaatttgatattaacctttagaacactgggctgaatgtcttctaatttgctgtaatcttttat--cagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG
















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|58018272|gb|CX705014.1|CX705014
EST:     TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT                         GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
EST: gi|214008165|gb|DB987056.1|DB987056
EST:     ATGTCAGCAGTCGCTCTT                         GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: ATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
EST: gi|208307969|gb|GE105449.1|GE105449
EST:     TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT                         GGTGCTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
EST: gi|209715079|gb|BW677122.1|BW677122
EST:     TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT                         GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
EST: gi|17518879|gb|BM187921.1|BM187921
EST:     TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT                         GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
EST: gi|209729539|gb|BW651866.1|BW651866
EST:     TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT                         GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
EST: gi|151400645|gb|EV270459.1|EV270459
EST:     TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGTTCTT                         GGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG
genomic: TGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTggtaatcttc ... ttgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatttacctgcttcactctttctctggtttaattgttgaaagattgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAAT
                            gtttaat  putative branch site (score: 4)
                             tttaattgttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtaatcttcatttttatggatatttacctgcttcactctttctctggtttaattgttgaaagattgtattacaGGTACTTCCTCAATCTGTTTGGATTAAGAGGATTGTTTAGTCTCATATTGGGTGAAGAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA