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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtattcttatggatatgttgattttttctacaaatgattgctgaacaaaaaatttaatggtggattcacgatgacattactgtctacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG

Basic information

species Glycine max
transcript GLYMA06G03230.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 7
gtattcttatggatatgttgattttttctacaaatgattgctgaacaaaaaatttaatggtggattcacgatgacattactgtctacatt-tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG
||     | |  || |||  |||||||  |      |||      || ||  |||  |     |   |  |  | |||| | |  |  || | || | |||||||||||||| |||||||||||||| |||||||| ||||||||||| || || ||||||||| |||| || ||||| ||||| || ||  |||| ||||
gtgcaggtgtt-atctgtgcattttttgcagctgacattttcattcataagcttttcttagtaaactaaaaaaatattattttgaaatttgtttgatatagGTTAAAATGATTATGGCAACAAACCGGCCTGATGTTCTTGACCCTGCACTTCTTCGTCCTGGGCGATTAGACAGAAAGATAGAGATTCCATTGCCAAATG

upper sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 7
---------------------------gtattcttatggatatgttgattttt----tctacaaatgattgc-----tgaacaaaaaatttaatggtggattcacgatgacattactgtc-tacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG
                           |||||| | ||| | ||    || |     ||| |||    |||      ||||  |    | |  | |  |||||   ||  | ||  |  | |  | |   | || |||| || ||||||||||| || || || |||||||| ||||| |||||| | || || |||||  | |||||| ||||||| ||||| || ||||||||||
gtactcttgactcttgaaaccattctggtattcat-tggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTGCTCCGGCCTGGCCGTTTGGATCGAAAAATTGAAATTCCACTGCCTAATG

upper sequence: GLYMA06G03230.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 7
gtattcttatggatatgttgattttttctacaa----atgattgctgaacaaaaaatttaatggtggattcacgatgacattactgtctacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG
|||  | |    | || |   |   | | ||      || || | ||| || | | ||  | |    |     |||    || |   | |  ||    || ||||| || ||||| |||||||| ||||| || ||||| |||||||||||||| || || |||||  | |||||| |||| || ||||| || || || ||||
gtagacctggaaaaatttctgtcaatgccacgttgccataatag-tgatcatagatttcgaggaaacaccgttgata--gttgccaac-atcttgtcattatagGTAAAGATGATCATGGCAACCAACCGGCCAGATGTTCTTGACCCTGCTCTTCTACGACCTGGTCGTTTGGATCGAAAGATTGAAATTCCACTACCAAATG

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|151393977|gb|EV263848.1|EV263848
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAG                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
EST: gi|24135574|gb|BU926084.1|BU926084
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAG                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
EST: gi|26058654|gb|CA801568.1|CA801568
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAG                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
EST: gi|254346176|gb|GR859789.1|GR859789
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAG                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
EST: gi|298164161|gb|HO013806.1|HO013806
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAG                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
EST: gi|254346175|gb|GR859788.1|GR859788
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAA-G                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
EST: gi|17023135|gb|BM094169.1|BM094169
EST:     CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAG                         GTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC
genomic: CGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatatttta ... tctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaaaatttaatggtggattcacgatgacattactgtctacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG
      atttaat  putative branch site (score: 4)
                                           tttctgtt  putative PPT
     aatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattcttatggatatgttgattttttctacaaatgattgctgaacaaaaaatttaatggtggattcacgatgacattactgtctacatttctgttgtagGTTAAAATGATAATGGCAACAAACCGACCTGATGTACTTGACCCTGCTCTCCTGCGTCCTGGGAGATTGGATAGAAAAATAGAAATCCCTCTGCCTAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - -cttatgg
- - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgtc