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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGATATCACCAATAGAAGTGGATGCTGTTCTCTTTCACATCCAGAAATTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataatttatttttggtttttacacaaatgtgctcaaaagttgagtaaatgaccattttttattagttctttgaagtttgtattcatcatatcttttttaacttttgatag

Basic information

species Glycine max
transcript GLYMA11G31310.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G31310.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0050g00390.t01 (Vitis vinifera), 5'ss of exon 3
AAAAGATATCACCAATAGAAGTGGATGCTGTTCTCTT-TCACATCCAGAAATTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataatttatttttggtttttacacaaatgtgctcaa----aagtt----gagtaaatgaccattttttattagttctttgaagtttgtattcatcatatcttttttaacttttgatag
|||||||||||||| |||||||||||||| || || ||||||||||| ||||||||||| ||||||||||| || || |||| ||| || || || |||||| | | || || || || |||| || || || || |||| | | | | | | |||| | | |||
-GAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAGACATTGCTCAAGCGGTTGCTTTTGGGGTTCCAGATGACAAATACGGCGAAGAGgtaagaaccgtaattccccattctttaattgctatcaacaccaatttattagaagggataaccaatgagatgaaatcatctccactttggacaaagcatg--------------------
















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|16277025|gb|BI942164.1|BI942164
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|16277773|gb|BI942555.1|BI942555
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|21256093|gb|BQ452981.1|BQ452981
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|21889797|gb|BQ743010.1|BQ743010
EST:     TTGCTCAAGCAGCTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|151406238|gb|EV276053.1|EV276053
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|16346137|gb|BI971732.1|BI971732
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|13125128|gb|BG315698.1|BG315698
EST:     GCTCAAGCAGTTGCTTTTGGAGTGACCTGATGCTCAAGTATGGAGAGGAG                         ATATATTTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGA
genomic: GCTCAAGCAGTTGCTTTTGGAGTG-CCTGATGC-CAAGTATGGAGAGGAGgtataattta ... cttttgatagATATA-TTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGA
EST: gi|58024866|gb|CX711607.1|CX711607
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|16105045|gb|BI892785.1|BI892785
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
EST: gi|58018249|gb|CX704991.1|CX704991
EST:     TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAG                         ATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG
genomic: TTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataattta ... cttttgatagATATATTGTGCTGTCATCCCAAGAGAAGGATCAAACGTTGATGAGGCAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGATATCACCAATAGAAGTGGATGCTGTTCTCTTTCACATCCAGAAATTGCTCAAGCAGTTGCTTTTGGAGTGCCTGATGCCAAGTATGGAGAGGAGgtataatttatttttggtttttacacaaatgtgctcaaaagttgagtaaatgaccattttttattagttctttgaagtttgtattcatcatatcttttttaacttttgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG