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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag

Basic information

species Glycine max
transcript GLYMA08G17000.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g42450.1 (Oryza sativa), 5'ss of exon 3
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag
 ||||||||||| ||||||||||| || || |||||  | || |||||||| || |||||||| || || ||||  ||||| |||||||||||||| ||||||   |||| |   |  |    | ||| ||  ||  |   |||| || ||||    | | ||| | |  | | | |  |  ||||||    |                                            
CAAGGGGAAGCAGAGCATTGGTTGCCTATTCTGGCTTCTTGCCAGGATGGTTCTCCAGATGCGTGGTACAATTCTCCCAGGACACAAGTGGGATGTCATGgta---tactcg---caatctaaactagtatcatgcctgtaatgtttggattctgaaatataatcactgatgtat-gttgtttttcctttttgtag-----------------------------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g08440.1 (Oryza sativa), 5'ss of exon 3
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag
 ||||||| | | |||||||| || || || ||||| || || |||||||| ||||||||| |||| ||||| |  || || |||||||||||||| ||||||       |  |   ||   ||| |   ||   ||  |  ||     |||| || ||| ||||     |  ||||     ||     |    | |   | ||   |                             
CAAGGGGAGGAACAGCATTGGGTGCCTGTTCTGGCTCTTGGCTAGGATGGTTCTGCAGATGAGGGGTACTATCCTCCCTGGCCACAAGTGGGATGTTATGgtatgcggtgttattacttcaagaacacgttgacattggaagtgc----attcatgaagataatttcatatcctttgtatgcttatacactgagtat-gtcttttgcag----------------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G126821_T02 (Zea mays), 5'ss of exon 2
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttcctttt-cggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag
 ||||||| | | |||||||| || || || ||||| || || |||||||| ||||||||| |||||||||| |  || |||||||||||||| || ||||||  || || | |  |  |   |   | ||||   ||  | ||||    | |||      | | |  ||| |  ||||     ||| |  | | |  |    ||   |                             
CAAGGGGAGGAACAGCATTGGATGCCTGTTCTGGCTTTTGGCCAGGATGGTTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAGGTCATGgtatgatgctagcttatgatgtcgttcaaaatgacattggagatgtgatgagtcc------agact--tataaccttggca---ttcttatatgataatgttgtttgcag----------------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G099657_T01 (Zea mays), 5'ss of exon 3
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag
 ||||||| | | |||||||| || || || ||||| || || |||||||| ||||||||| |||||||||| |  || |||||||||||||| || ||||||   ||  |  |  |  |  |   | ||||   ||  | ||||  ||  | |  |     ||| |||  ||||        ||| |    | |  |||  |   |  |                           
CAAGGGGAGGAACAGCATTGGATGCCTGTTCTGGCTTTTGGCCAGGATGGTTCTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAAGTCATGgtatgctagcttatgatgct--gtccaaaatgacattggagatgtg-gtgattccatgttttattggtaacatttcca-----ttcttatttgataataatgtcgtttgcag-------------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G145308_T01 (Zea mays), 5'ss of exon 3
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaata-cttgt--tccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag
 || |||| | | |||||||| || || |||||||| || || ||||||||  |||||||| |||||||||| |  || |||||||||||||| || ||||||   || ||| |  | || |||  |||   || ||| |    ||  | |  ||  |    ||| |  | ||| || |  |    |      | | | ||  ||                                   
CAAAGGGAGGAACAGCATTGGATGCCTGTTTTGGCTTTTGGCCAGGATGGTTTTGCAGATGAGGGGCACTATCCTCCCTGGGCACAAGTGGGAAGTCATGgtatgctagcttatgatgctgttcaaaatgacattgtgatg---attccaggttttattggtaaactctgcattcttatatgacaata-----atgttgtttgcag----------------------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G092719_T01 (Zea mays), 5'ss of exon 3
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag
 ||||||| | | |||||||| ||||| || |||||  |  | |||||||| ||||| ||| |||||||||| | ||| |||||||||||||| || ||||||   | || | |           ||    | ||||  | ||| |  ||    || |   | |    ||| ||||||  |  ||            | | | |  |   |  |                       
CAAGGGGAGGAACAGCATTGGATGTCTGTTCTGGCTTCTGTCCAGGATGGTTCTGCAAATGAGGGGCACTATCCTTCCTGGGCACAAGTGGGAAGTCATGgta---tgctagct-----------tatggcgctgttcaaaatgacattagagatgcaatgagtccagatttttttggtaacctttgcattcttgtatgataatgctgtttgcag----------------------

upper sequence: GLYMA08G17000.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0002g00610.t01 (Vitis vinifera), 5'ss of exon 3
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaa-atacttgtt--ccttttcgga----ataga----atggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag-------------------------------------------------
 ||||| ||||| |||||||| ||||| || ||||| || ||||||||||| |||||||||||  ||||||||  ||| || |||||||||||||| |||||||| |||   |    || ||| ||     ||||     |  || || | |   |||| |||   | |  |      ||  | |||  | | | | ||| | | |   |   ||   |  |  ||   | |  ||   |    |  |                                                 
CAAGGGAAAGCACAGCATTGGCTGTCTGTTCTGGCTGTTGGCAAGGATGGTTCTGCAGATGCGTCGCACTATTGCTCCCGGACACAAGTGGGATGTGATGgtaaagatatcagaaaaccattttgggttttatagttcatacagtattatttgcttctgaattgacgcatgacgaatttacaagtttttgcactgtactg-aggtttacatttttg--agtttgatgatttagcttgccccctggtggatgattacttgatgattttgacttaccatgatctttcctcgatatgtag

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|5606682|gb|AI900780.1|AI900780
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|208152036|gb|GD944339.1|GD944339
EST:     GCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: GCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|193567272|gb|FK526941.1|FK526941
EST:     GGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: GGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|9900814|gb|BE609782.1|BE609782
EST:     GCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: GCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|15286900|gb|BI470791.1|BI470791
EST:     TACTGCAGATGCGGGGCACTATTCGT-CATTTCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|23052768|gb|BU577259.1|BU577259
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|15663312|gb|BI700683.1|BI700683
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|6719412|gb|AW307059.1|AW307059
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|192304648|gb|FG994940.1|FG994940
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|20075735|gb|BQ094518.1|BQ094518
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|193570031|gb|FK525774.1|FK525774
EST:     GGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: GGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|27425246|gb|CA936766.1|CA936766
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|4302114|gb|AI443287.1|AI443287
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|193453911|gb|FK419106.1|FK419106
EST:     GCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAG
genomic: GCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAG
EST: gi|6952276|gb|AW424344.1|AW424344
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|208207621|gb|GE007570.1|GE007570
EST:     GGGCACAAGTGGGATGTAATG                         GTGGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGA
genomic: GGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGT-GGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGA
EST: gi|22540297|gb|BU090140.1|BU090140
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|208045129|gb|GD843233.1|GD843233
EST:     GGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: GGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|15663310|gb|BI700681.1|BI700681
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|208162182|gb|GD965293.1|GD965293
EST:     GGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: GGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|151405528|gb|EV275342.1|EV275342
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|22540179|gb|BU090022.1|BU090022
EST:     TACTGCAGATGCGGTGCACTATTCGTACAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTT
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTT
EST: gi|192304647|gb|FG994939.1|FG994939
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|208222573|gb|GE017378.1|GE017378
EST:     GGGCACAAGTTGGGTATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGA
genomic: GGGCACAAG-TGGG-ATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGA
EST: gi|58020333|gb|CX707075.1|CX707075
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
EST: gi|6846843|gb|AW349133.1|AW349133
EST:     TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATG                         GTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA
genomic: TACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatact ... tcttatgcagGTGGATTTATTCTTCTATAGAGAACCTGAAGAGGCCAAGCAACAAGAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGGGGAAGCATAGCATTGGTTGTCTCTTTTGGCTATTAGCAAGGATGGTACTGCAGATGCGGGGCACTATTCGTCCAGGGCACAAGTGGGATGTAATGgtaaaatacttgttccttttcggaatagaatggtgttttatatgtctgtattcctgtagaaaattagtattattttggggagtttcctgcaagctcttaacattaataactaaatatctcaaatttttcttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG