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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaagatctattgccattgtttatttttgaagcttcttcttcatctcatcgttggatcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

Basic information

species Glycine max
transcript GLYMA04G39940.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g60790.1 (Oryza sativa), 3'ss of exon 1
gtagaagatctattgccattgtttatttttgaagcttcttcttcat-ctcatcgttgga--------tcatgttgttgttt----gtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
|||     |   || ||  || |||      |   | |||        ||| || || |        || | ||| ||  |    | |||| ||||||||| | ||||| || |||||||| ||||| |||||||||||||||| ||| || ||||||||||||| ||| |||||||| |||
gtaaggccttgcttccctatgcttaacgcctagattgctttgcgggattcagcgctgaactgacctctcttcttgctgcatcggcgcagACCTTCAAGCGCCGCAATGGCGGCCGCAACAAGCACGGTCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g39960.2 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------gtagaagatctattgccattgtttatttt--tgaagcttcttcttcatctcatc--gttggat-catgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
                                               |  |  | |     | | |  | |  |    | || || |   ||  || | ||   |||| | | |  | |   | | |||| |||||||||||||| || || |||||||| || ||||||||||| || |||| ||| || ||||||||||||| ||| |||||||| |||
gtaaggagctcgccgcttccggatccaccctagccgccgcggcggcggcggccgcttcggcgtcttcttcttctccgctcaatctcccggttagtcccttctgattggtttcctcctttccctcgcagACCTTCAAGCGCAGGAACGGCGGCCGCAACAAGCATGGCCGCGGCCATGTGAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899149_T02 (Zea mays), 3'ss of exon 1
gtagaagatctattgccattgtttatttttga-agcttcttcttcatctcatcgttgg-atcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG-------
||      |      ||| | |   || | |    | |   | ||    | | ||||   ||  ||||  |   | |||| |||||||| |||||||| || |||||||| ||||| |||||||||||||||| ||| || ||||||||||||| ||| |||||||| |||       
gtgagttcttcgagaccaatctcccttctcgccgacgttgccgtctaacctttgttgttgtctggttgccgcc-gcagACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAGGTAACAC

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G899149_T01 (Zea mays), 3'ss of exon 1
gtagaagatctattgccattgtttatttttga-agcttcttcttcatctcatcgttgg-atcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
||      |      ||| | |   || | |    | |   | ||    | | ||||   ||  ||||  |   | |||| |||||||| |||||||| || |||||||| ||||| |||||||||||||||| ||| || ||||||||||||| ||| |||||||| |||
gtgagttcttcgagaccaatctcccttctcgccgacgttgccgtctaacctttgttgttgtctggttgccgcc-gcagACGTTCAAGCGGAGGAATGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATCCGCTGCTCCAACTGCGCCAAGTGCTGCCCCAAG

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G129015_T02 (Zea mays), 3'ss of exon 1
----------gtagaagatctattgccattgtt---tatttttgaagcttcttcttcatctcatcgttggatcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
          | |||  ||||    ||   ||      |    |  ||| ||   | | |   || || | |  |  || |    | |||| |||||||| ||||| || || |||||||| ||||| |||||||||||||||| ||| || ||||||||||||| ||| ||||| || |||
gtgagctatcggagaccatctccgtcctccgtcacgcctcgccgccgctgctgtctaaccctttcttttgttggttgtggttgccgcagACGTTCAAGCGGAGGAACGGCGGACGCAACAAGCACGGGCGCGGCCACGTCAAGTACATACGCTGCTCCAACTGCGCCAAGTGCTGTCCAAAG

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G40590.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagaag-atctattgccattgtttatttttgaagcttcttcttcatctc--atcgttgga-tcatgttgttgtttgt-----agACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
|||     ||  || |   ||| |||| ||||||      |    ||     || | ||   |    |||||||||||     ||||||||||||| ||||| || ||  | ||||| |||  | | || ||||||||    ||  ||||||||||||||||||||||||||||||||
gtactctcattcatcg--gttgcttatctttgaattacaataaagatagagaattgatgatcttccattgttgtttgtgttgcagACTTTCAAGCGAAGGAACGGTGGGAGGAACAAGCACAACAGAGGACACGTCAACCCAATCAGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g07940.t01 (Vitis vinifera), 3'ss of exon 1
gtagaagatctattgccattgtttatttttgaagcttcttcttcatc-----tcatcg-----ttggatcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
|| || | | |  |   |   || | |||| || |||  |    |||     ||| ||     || | | ||  |||| |||| |||| |||||||| |||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||
gt-gaggttttcctcgaaaatttcacttttcaatcttgcttgctatcatttctcaccgatttttttggtaattgtgtt-tttgcagACGTTCAAGCGAAGGAATGGTGGTCGCAACAAGCACGGCCGCGGCCACGTCAAGTTCATTCGCTGCTCCAACTGTGGCAAATGCTGCCCTAAG

upper sequence: GLYMA04G39940.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0067g02700.t01 (Vitis vinifera), 3'ss of exon 2
gtagaagatct-----attgccattgtttatttttgaagcttcttcttc---------atctcatcgttggatcatgttgttgtttgt-----agACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
|||  |  |||     ||  |||||         | || ||||||||||         || | | | |   ||   ||| ||  ||||     |||| ||||||||||| || || || |||||||| |||||||| || || ||||||||||| || ||||| |||||||| ||||||||||| |||
gtaagatctctcaaccatcaccattaccctcaactcaatcttcttcttctccgttgtgatgtaaccttcaaatttcgttattacttgtgctgtagACGTTCAAGCGCAGAAACGGCGGCCGCAACAAGCACGGCCGTGGACATGTCAAGTTCATCCGCTGCTCAAACTGCGGAAAATGCTGCCCAAAG

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|254317610|gb|GR826594.1|GR826594
EST:     TCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|4307186|gb|AI444011.1|AI444011
EST:     GTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|38191905|gb|CF921111.1|CF921111
EST:     CTAAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: CTAAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|13791368|gb|BG653959.1|BG653959
EST:     GTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|16348589|gb|BI974184.1|BI974184
EST:     TCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGGAACAAACACGGACGCGGCCACGTC
genomic: TCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|213594186|gb|DB963783.1|DB963783
EST:     AAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: AAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|193344833|gb|FK310409.1|FK310409
EST:     AAATAGAGTAGTTTCGTTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: AAATAGAG-AGTTTCG-TTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|17022066|gb|BM093100.1|BM093100
EST:     TTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|16348736|gb|BI974331.1|BI974331
EST:     GTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|7147457|gb|AW509379.1|AW509379
EST:     TTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|21889162|gb|BQ742375.1|BQ742375
EST:     GTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|151411660|gb|EV281471.1|EV281471
EST:     AAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: AAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|4289414|gb|AI441472.1|AI441472
EST:     CGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: CGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|7041796|gb|AW471690.1|AW471690
EST:     TTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|6072231|gb|AW101618.1|AW101618
EST:     TTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|9901209|gb|BE610177.1|BE610177
EST:     TTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|17963317|gb|BM270076.1|BM270076
EST:     GTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|254317611|gb|GR826595.1|GR826595
EST:     TTCGTCA-CATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|193433735|gb|FK399705.1|FK399705
EST:     AAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: AAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|15815421|gb|BI787696.1|BI787696
EST:     TTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|151412448|gb|EV282260.1|EV282260
EST:     CTAAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: CTAAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|209725822|gb|BW659938.1|BW659938
EST:     CTAAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: CTAAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|10709737|gb|BF009461.1|BF009461
EST:     TTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|31463666|gb|CD405694.1|CD405694
EST:     GTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|4313736|gb|AI460855.1|AI460855
EST:     TTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|31457848|gb|CD399876.1|CD399876
EST:     GAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: GAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|6847660|gb|AW349950.1|AW349950
EST:     GTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGNCGCAACAAACACGGCCGCGGCCACGTC
genomic: GTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|298175442|gb|HO015075.1|HO015075
EST:     AAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: AAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|208324970|gb|GE124868.1|GE124868
EST:     CTAAATAGTAGAGTTTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: CTAAATAG-AGAG-TTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
EST: gi|193363921|gb|FK331701.1|FK331701
EST:     AAATAGAGAGTTTCGTTCGTCACCATG                         ACTTTCAAGCGC
genomic: AAATAGAGAGTTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGC
EST: gi|31459779|gb|CD401807.1|CD401807
EST:     TTTCGTTCGTCACCATG                         ACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC
genomic: TTTCGTTCGTCACCATGgtagaagatc ... ttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttttgaagcttcttcttcatctcatcgttggatcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG
     ttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaagatctattgccattgtttatttttgaagcttcttcttcatctcatcgttggatcatgttgttgtttgtagACTTTCAAGCGCAGGAATGGAGGTCGCAACAAACACGGCCGCGGCCACGTCAAGTTCATTCGATGCTCCAACTGCGGCAAATGCTGCCCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC