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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggccgactaaacagggatcaattgaacaatgttattttcttgatcacttgtgtctgaagtgtgttctaatggcttagtgaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG

Basic information

species Glycine max
transcript GLYMA10G35560.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 9
gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgat--attggccgactaaacagggatcaattgaacaatgttattttcttgatcacttgtgtctgaagtgtgttctaatggcttagtgaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
                       |    || |     || |  || ||   |||    | |        || |  ||  || ||  |  | |||    ||| |  ||   | |     |||||  ||| |||          ||| ||    |  ||||| ||||| |||||||||||||||||||| |||||   ||||||    ||||||||||| ||||| || || ||  | |||
----------------------gtaattgaattaatctg-cacataattagttgatttattttttgcaaat-agctgtgca-tgccaactactttgctactggcctc---aatactaactaataactt-gtg-------cccagGTACTGACTACACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGAACAAGAACTAATCGTTCAGGCGGTGTGCAG

upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 9
gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggcc-gactaaacagggatcaattgaacaatgt---tattttcttgatcacttgtgtctgaagtgtgttctaatggcttagtga-----aatta-ttat----agGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
|||   || | |  | || ||| | |||  |      ||  | ||  | ||  |  || || ||| |||  |  |  |   ||    |   |  |||      | ||  || ||  |  ||||  |  | | | |     ||| | || |    ||| ||    || ||||| ||||| |||||||||||||||||||| |||||   ||||||    || ||| |||| |||||||| || ||  | |||
gtaaggaatcattttcatttatgt-tcctggaaaaaatggatcattttgtttccttgaatacacaaggaatatgtacattttgcacatgactagttggcgttgtttgcatgcagcctactctacagtttgactaattcctaataacttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG

upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 9
gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggccgactaaacagggatcaattgaacaatgttattttcttgatcacttgtgtctgaagtgtgttctaatggcttagtgaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
                                                    |   |  ||       |    |   |  |||    |     ||||      | || ||  |||   |||         |         ||| ||||||||||||||   |||||| ||||||||||||||||  |||||| ||||||  | | | || ||||| || || |||||||| || |||
----------------------------------------------------gtatagaaagttatacttttctctcctttgtccaatctaaaatcaacctcctttggagc-tgtataaatcatacgcaaatgaacccgcagGTACCTTTTTGACTGGTCTTGAACACAATGATGAGTTCTATACCGATGAAAATGGAAGAATACGTACCAGAACCAACCGATCTGGTGGAATTCAG

upper sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 9
----------------------gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggccgactaaacagggatcaattgaaca--atgttatt-ttcttgatcact--tgtgtctgaagtgtgttctaatggcttagt----gaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
                       |  | | | || | |    | || |   | |     ||  | |  | ||||      | ||  |  || |  || |    ||||| |  |||||  |   |  | | |||    | | ||| ||    |||      ||| ||  |  ||| || ||| ||||||||||||||||||||||||||||||  |  |||| |||||||   |  || |||||||| |||||||||||||||||||||
gtagagaaacttttggtgctttttggttatattttcctccaaa-attttaaatttggggtggataactagattgattatttgaattgcaattatatgcatcttatgttgtcattcttccttgatattatttctttgttat-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|16276418|gb|BI941848.1|BI941848
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|16276792|gb|BI942046.1|BI942046
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|193486868|gb|FK450449.1|FK450449
EST:     TTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|120532705|gb|EH260838.1|EH260838
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|10843361|gb|BF066663.1|BF066663
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|254333630|gb|GR848548.1|GR848548
EST:     ATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: ATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|33387796|gb|CA851003.1|CA851003
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|16277466|gb|BI942396.1|BI942396
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|19053065|gb|BM731732.1|BM731732
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|19268860|gb|BM885116.1|BM885116
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|16282970|gb|BI945300.1|BI945300
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|208201922|gb|GD997013.1|GD997013
EST:     TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC
EST: gi|7691321|gb|AW759514.1|AW759514
EST:     AATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAG                         GCACCTTTTTGACTGGGAGTGAACACAATGATGAGTTCTATATAGATGAAC
genomic: TATGTCATTGCCTGCAACCAAGGGCTTTCAGTTTGGTAGTGGGTTTGCAGgtactaaaac ... attattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgatcacttgtgtctgaagtgtgttctaatggcttagtgaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
                           ttctaat  putative branch site (score: 2)
                                     ttagtgaaattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggccgactaaacagggatcaattgaacaatgttattttcttgatcacttgtgtctgaagtgtgttctaatggcttagtgaaattattatagGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG

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