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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaaacttgcttatttatacatctgagtgcctttgtctatgattttgactgactaaacagggatcaattgaacaatgttattttcttgatcacttatatctgaggtgtgttctgatggcttagtgaaatcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 9
gtactaaaacttgcttatttatacatctgagtgcctttgtctatgattttgactgactaaacagggatcaattgaacaatgttattttcttgatcacttatatctgaggtgtgttctgatggcttagtgaaatcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
                                     | |  |   || |   |  ||   |   |  ||||  || |      |  | | || |     | | | |    |   |  |||         || |     ||| ||||||||||||||   |||||||||||||||||||||||  |||||| ||||||  | | | || ||||| || || |||||||| || |||
------------------------------------gtatagaaagttatacttttctctcctttgtccaatctaaaatcaacctcctttggagc-----tgtataaatcatacgcaaatg---------aacc--cgcagGTACCTTTTTGACTGGTCTTGAACACAATGATGAGTTCTATACCGATGAAAATGGAAGAATACGTACCAGAACCAACCGATCTGGTGGAATTCAG

upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 9
------------gtactaaaacttgcttatttatacatctgagtgcctttgtct-------atgatt---ttgactgactaaacagggatcaattgaaca--atgttatt-ttcttgatcact--tatatctgaggtgtgttctgatggcttagt----gaaatcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
             |  |     ||| |||| | | | ||  |     |   | |       || | |   |||| |   | ||  |  || |  || |    ||||| |  |||||  |   |  ||| |||  | | | |||  |    |||      ||| |   |  ||| || ||| |||||||||||||||| |||||||||||||  |  |||| |||||||   |  || |||||||| |||||||||||||||||||||
gtagagaaacttttggtgctttttggttatattttcctccaaaattttaaatttggggtggataactagattgattatttgaattgcaattatatgcatcttatgttgtcattcttccttgatattatttctttgttat-ttccaactatttatcattggaagttcctgcagGTACATTTATGACTGGGAGTGAACATAATGATGAGTTCTTCACGGATGCACATGGACGAATCAGGACAAGAACTAATCGCTCTGGTGGGATACAG
















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|58017502|gb|CX704244.1|CX704244
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... atcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
EST: gi|23052733|gb|BU577224.1|BU577224
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... atcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
EST: gi|16346555|gb|BI972150.1|BI972150
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAA
genomic: AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... atcattatagGCACCTTTTTGACTGGGAGTGAA
EST: gi|120533980|gb|EH262113.1|EH262113
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... atcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
EST: gi|19934393|gb|BQ079423.1|BQ079423
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... atcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
EST: gi|254340229|gb|GR858354.1|GR858354
EST:     AGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: AGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... atcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgatcacttatatctgaggtgtgttctgatggcttagtgaaatcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
                           ttctgat  putative branch site (score: 3)
                                           aaatcattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaaacttgcttatttatacatctgagtgcctttgtctatgattttgactgactaaacagggatcaattgaacaatgttattttcttgatcacttatatctgaggtgtgttctgatggcttagtgaaatcattatagGCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG