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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG

Basic information

species Glycine max
transcript GLYMA15G12780.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 2
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
                        | | || |   |||| |  | || ||   |    | | ||     |   || ||    |  | | ||  |   |||| ||    ||     ||||||||||||| || ||||||||||| |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||| |||||  ||
--------------------gtaatgttttctccaaatgct--atcttgtaggatgtttgttagccaagtgaagttatatgctaagtgtggcaccactgatggttc--tgcataattttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCTCAAACACGACGTGGCCAGCCTTGCTGGTTTAGGGTGCCTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g50050.1 (Oryza sativa), 3'ss of exon 3
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
                     |    |  |  ||| |||||| |   |  |   ||  |   | |    || |   |    |||        | ||    ||||   |||| |     ||||||||||||| |||||||| ||||||||||| || ||||||||||| || || || || ||  | || || ||||||||  | ||||||
---------------------gtacatgatacttgtatgatttagtgacctgggattatgaaacaacaatattagcaaaatattttctaaactttt----ttgttctttga-gtaacctgcagCTTCAGGCCTATTTTCTGGTTCTTGATGATATAATGGATAACTCACAAACTCGACGAGGAAAACCCTGTTGGTTTAGGCTTCCCAAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g46580.1 (Oryza sativa), 3'ss of exon 3
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
                                   |||| || |||     || | | || |  ||  |   ||  |    | |      | || | | |   | |  || ||   | || ||||||| || || ||||| || |||||||| || |||||| | |||||||| || ||||||||||| || |||||| | |||||  ||
---------------------------------gtaatgctttaac-----ctcaactttccgaataatgggtgcaaatcaactaaaattgctcctctaagc-tttactgttgt-ctatgtagCTTCAAGCTTACTTTCTCGTGCTTGATGATATCATGGATGATTCTCACACTCGACGTGGTCAGCCTTGTTGGTTTCGGGTGCCTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 2
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagat-gtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
               |   | |    |  ||||||  |  |   |  | || ||||  |   |||| |  |  | || |    |     || || |||  |||  || ||  | | | || |||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| |||||||||||||||||  ||
---------------gtactagttccttctgtttgttttct---atcatttttaatattaatagattgcattttctgctaattt-----ggaatttta--attcactatttcttg-tcttacagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAGCCTTGCTGGTTTAGAGTGCCACAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 2
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
                  |    ||| ||| | ||     || ||  | || | ||  |  ||||   | | | |  ||  | |  |     |   || | | | | ||      | ||||||||||| || ||||||||||| |||||||| |||||||| ||||| || ||||| ||||| || || |||||||||||||||||  ||
-----------------gtactacttacttctgtgttgctttcaagcattttttatgttaacagaa--tgaattttctgctaatatgaaattttaaatcactatttctta-----tcttgcagCTTCAAGCTTATTTTCTTGTGCTTGATGATATTATGGACAACTCCCAGACACGGCGTGGCCAACCTTGCTGGTTTAGAGTGCCACAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168681_T01 (Zea mays), 3'ss of exon 3
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
                     |  ||| || |||        |  ||  | | |        | |||    | || | || | || | | |  || ||    ||  | |  | |  ||| ||||||||||| |  |||||||| |||||||| || |||||| |||||||||| || || || ||||| |||||||| || |||||  ||
---------------------gtatttttttttttgtccccca--ctgttgccaggaa----aaatgc---cagtcaaggaactgagagtgg-ctcatctaagttcgctcgtcgtattt-cagCTTCAGGCTTTCTTTCTTGTGCTTGATGATATCATGGATGACTCTCACACTCGTCGCGGCCAGCCTTGCTGGTTCAGGGTGCCTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG-------------
                                                    ||||    ||   |  ||    |  |  | ||       ||  |    |||| | ||| | |  |||||||||||| || ||||| ||||| ||||||||||| ||||| ||||||  |||||||||||| ||||| || |||||||||  ||| |||             
---------------------------------------------------gtaatt-cctcttttacttctcttcttatctttcatctcaatgctcattttgtat-ttgcttgcatttgcagCTTCAAGCTTATTTCCTTGTGCTTGATGACATCATGGACAACTCTGTCACACGCCGTGGCCAGCCTTGTTGGTTTAGAAAGCCAAAGGTTGGTATGATTG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
||||  |  |   ||    ||  | ||    | |  || | |||  |||   || ||   ||      |   | ||  |  ||          || || |     | || ||    ||||||||| || || ||||| ||||| |||||||| |||||||||||||||  ||| ||||||||||| || |||||||| ||||| ||  ||
gtataccaatgataaagacttatcctttcaatctctattagtaa--taga--tactctcctctctctctctttatgtcgctatca--------ctcatca-----tattcattatctttgcagCTCCAAGCTTATTTCCTTGTGCTTGATGATATTATGGATAACTCTGTCACTCGCCGTGGTCAACCTTGCTGGTTCAGAGTTCCTCAG

upper sequence: GLYMA15G12780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0015g01010.t01 (Vitis vinifera), 3'ss of exon 3
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgt-ttactgtgatggcattgggg---gggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
||| |||    |||  | |   ||| | || | | || | | || ||  |||| |       |    |   | |||   |   |||  |   |  |  |||||  |   | |  |||    ||||||||||| |||||||| ||||| |||||||| |||||||||||||| || ||||| || ||||| || |||||||| || || ||||||
gta-ggcaacagaatacctcc-cctgtattttgttaaggctgaagctttttctcaggtccataatcataccagtgtatcgcttttgttgcatgacaatttatgccttcttttctatgccacttgcagCTTCAAGCATATTTCCTTGTGCTTGATGATATTATGGATAACTCGCATACACGTCGAGGTCAACCTTGCTGGTTCAGGGTTCCCAAG

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|298187383|gb|HO034532.1|HO034532
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCGCACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|298187020|gb|HO034169.1|HO034169
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|13789758|gb|BG652349.1|BG652349
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|9902003|gb|BE610971.1|BE610971
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|192294520|gb|FG987449.1|FG987449
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|19345889|gb|BM890769.1|BM890769
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|298181906|gb|HO026081.1|HO026081
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|5606131|gb|AI900229.1|AI900229
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|193581203|gb|FK535486.1|FK535486
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|208272802|gb|GE066266.1|GE066266
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|15814471|gb|BI786746.1|BI786746
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|14259182|gb|BG882090.1|BG882090
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|208302800|gb|GE097933.1|GE097933
EST:     TTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATA-TTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: TTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
EST: gi|6071532|gb|AW100919.1|AW100919
EST:     ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGG                         CTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA
genomic: ATGATGACGAAATTTTTCATGCCAGTGCTCTTGGTTGGTGTATTGAATGGgtatggctgt ... ggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG
                                     tgttgat  putative branch site (score: 4)
                          ttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggctgttgaaagcttttgcctttcttgtttgaatgattaaactagttctaatcgtttcagatgtttactgtgatggcattgggggggatcttatgattgtctgttgatgggttttgcagCTTCAGGCATATTTTCTTGTTCTTGATGACATTATGGATAACTCTCACACACGCCGTGGTCAGCCATGCTGGTTTAGAGTGCCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG