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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaatcagtttctttaataagattcactttcagtatttgagacaaatatgaaatacctcatatttaatctagctagtgaaccattgtgtttctttacaactacttag

Basic information

species Glycine max
transcript GLYMA10G34370.1
intron # 6
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G34370.1 (Glycine max), 5'ss of exon 6
lower sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 6
ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaatcagtttctttaataagattcactttcagtatttgagacaaatatgaaatacctcatatttaatctagctagtgaaccattgtgtttctttacaactacttag
| |||    ||||| || ||| | || |  ||||| || |||||| |||| ||||| || ||||||||||| |||||||||||  |  |   | ||   |||    | | |       || |  | | | |  | |   |    |  | ||| | |||        |   |||||||    |  |||  
AGTCCACTTGATGTTGATAAGCTTCGGAAGATTGGTGTCAAAACTGTATTCTGCTTGCAGCAAGATTCAGATCTTGAgtatccccactaacatttt--gtaa----cgcgtct----cttaaagctagtct--actgatttggctaaactctcgatagcttctttctcgttttctttggtcccgcttgt

upper sequence: GLYMA10G34370.1 (Glycine max), 5'ss of exon 6
lower sequence: AT3G52180.1 (Arabidopsis thaliana), 5'ss of exon 5
ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaatcagtttctttaataagattcactttcagtatttgagacaaatatgaaatacctcatatttaatctagct-agtgaaccattgtg-----tttctttacaactacttag--
|| ||||||||||| |||||| | |||| ||||||||| ||||| ||||||||||| ||||||||| ||||||| |||||||||    |    || |  |    ||||   | |  ||||       |  |    | | ||  ||| | |   |   | ||| |    |||     |  ||| || | | |||    
ACCCCTGAAGATGTTGACAAGCTTCGTAAAATTGGAGTTAAAACCATATTTTGCTTGCAACAAGATCCAGACCTGGAgtatccttccaaagccctctttttctgttcatgattatgattttgttttcactt----tccttcgcattgagtgaggaagaatgatctgcagtgcagaatgccttgaccaatccttccag

upper sequence: GLYMA10G34370.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 6
ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaatcagtttctttaata-agattcactttcagtatttgagacaaatatgaaat---acctcat-atttaatctagctagtga-accattgtgtttctttacaactacttag-------------------------
| ||| |||||||| |||||| | || || ||||| |||||||| || ||||||||||||||||||||||| |||||||||||||| || |||  ||  || || |||| ||  | ||| |   | | || |    |   | | | | | ||||   | ||| ||| |  ||||| |   |    || |||   |                         
AGTCCAGAAGATGTTGACAAGCTTCGGAGTATTGGGGTGAAAACCATTTTTTGCTTACAACAAGATTCAGATCTTGAgtatcctaaacaattttattgttagagtttcatttggactatctattatatatttagcttttgatcacttgagttaagacaactactgacaaaattgtctgagtgaggaagtacactgttaattccttgacttgtatgtccag

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|120532166|gb|EH260299.1|EH260299
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA                         ATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|17022153|gb|BM093187.1|BM093187
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA                         ATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|193463792|gb|FK427016.1|FK427016
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATCCAGACCTTGA                         ATATTTCGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|9564018|gb|BE473527.1|BE473527
EST:     GCTTACAACAAGATTCAGACCTTGA                         ATATTTTGGAGTTGATATTAATGCCATACGAG-A-ATGCCAAGACATGCAA
genomic: GCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|24205361|gb|BU964614.1|BU964614
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA                         ATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|209709966|gb|BW681009.1|BW681009
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA                         ATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|6916528|gb|AW398058.1|AW398058
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATCCAGACCTTGA                         ATATTTCGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
EST: gi|7589574|gb|AW705345.1|AW705345
EST:     AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGA                         ATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA
genomic: AGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaat ... aactacttagATATTTTGGAGTTGATATTAATGCCATACGAGAATATGCCAAGACATGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTCCTGAAGATGTAGACAAGTTGCGTAGAATTGGAGTGAAAACTATATTTTGCTTACAACAAGATTCAGACCTTGAgtatcctaatcagtttctttaataagattcactttcagtatttgagacaaatatgaaatacctcatatttaatctagctagtgaaccattgtgtttctttacaactacttag

- - - - - - - - - - - - - - -  TTGGAG