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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggttttatgttctatctattgagtagcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG

Basic information

species Glycine max
transcript GLYMA20G38810.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g61860.1 (Oryza sativa), 3'ss of exon 9
gtcaggttttatgttctatctattgagtagcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgt-acactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
                               ||  |    | ||  ||     | |||      | | ||    |  | | | | |||      |  | | |  |  |  ||||  ||| |    | |||||| |||||||| |||||||||||||| ||||| ||||| || || ||||||||| |||| ||  ||||  |||||||| | ||||
-------------------------------gttacaatctctttttttttgtacttgatctaataatatatctagctattatattatctcgaaatatgcttaatacttaattgctatt-tgaacatttcagTCCTTCGAGTTTGGGATGTGCTTCTGTTTGATGGAAATCGCGTGATGCTCTTTCGAACAGCTCTTGCCCTAATGGAGTTGTATG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G096470_T01 (Zea mays), 3'ss of exon 9
gtcaggttttatgttctatctattgagta-gcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttgg-acttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
                         |||| || | |  || ||||   |  |    |||  | |     || |||  || |   || | |    |  ||| |     | || ||  ||| ||    | |||||| ||||| ||||||||||| ||||| ||||| |||||||| || ||||| ||  | || ||  ||||  | |||||| | ||||
-------------------------agtatgcttggactaatattctgtttc----ttg--agtagactataagctattatcttctctaga--aacattcttagcattttactgctatttttaaacatttcagTGCTTCGTGTGTGGGATGTTCTTCTCTTTGAGGGAAACCGTGTGATGCTGTTCCGGACAGCTCTTGCACTGATGGAGTTGTATG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 9
gtcaggttttatgttctatctattgagtagcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttgg-acttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
            ||    | | | ||     | |  |||   ||   |   | ||     ||  |    |    | |  |||    || |  ||   ||  ||| |  |||     || ||||| |   |||||||  ||||||||||||||||||| ||||||||||| || || ||||| || ||||| ||| | || || |||||  | ||||
------------gtcaggtttttagaaattggaattttaaactttacttttagag----gaaaattgtttatatactcttacg---ttttctgaatgtcagtctcaaatatc----ttctttggtataacagTTCTCAGAGTGTGGGATGTGCTTCTATTTGAAGGAAATCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAATTTTATG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 9
-----------------------------gtcaggttttatgttctatctattgagtagcg---tagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
                             |||  |||| |  |   ||  | | | |||     ||   | | | |   | | ||  |   ||   |    |  |   ||    |||      | |  ||| |||| |   ||  |  |  | | ||   |||||||| |||| |||||||||||||| ||||||||||  || || ||||| || ||||| ||| | || || ||||| |||||||
gtcaggttttaaacattggaattaaagctgtcttgtttgaaatagaattgagtaactagtaaattatgctggcaatctgttaaaatttgatcatctttctctttgagatttgggactgagaacccattttctttctaa---atgttcgtcttcttgatcacagTTCTTAGAGTCTGGGATGTGCTTCTCTTTGAAGGAACTCGTGTTATGCTTTTCAGAACAGCACTCGCATTGATGGAACTATATG

upper sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------gtcaggttttatgttctatctattgag--tagcgtagcttagtattgcttcacaaa-------gttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
                                                 |  ||  || |   ||||||| |   |    |   |||        |||| ||        ||  || |||||     |||||  ||   | ||| |          |  | | |  ||   || |   |||||||||||| || || ||||||||||||||||||||||||||||| |||||||| |||| ||| ||| ||||||| |||||| ||||||
gtcagtctccatcatggcttatatagaaattagatgttatttggggcctacattgcatttaaaatctatttatatttctttgatttatggccatctcactaatcttagcattctcattgtcatgattgcattcataatgtcttggttacaagcttatgggttttgatggctttctcctgacttcagTTCTCCGGGTCTGGGATGTGCTTCTTTTTGAAGGAAACCGTGTCATGCTATTTAAAACAGCACTTGCTTTGATGGAGTTATATG

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|120496536|gb|EH224703.1|EH224703
EST:     TGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAAGTGGTCAG                     
genomic: TGGACCATGGTTCCTGTCCATTTTTGTGAACATGCTTCCTTGGGAAA---GT--Ggtcaggtttt ... tggact






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG
                        ttctgat  putative branch site (score: 3)
                             atctattgtaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggttttatgttctatctattgagtagcgtagcttagtattgcttcacaaagttgccaatgtcaaatgagcatttgtacactattgttcgagcttccttctgatctattgtaattatttggacttcagTTCTTCGAGTGTGGGATGTGCTTCTTTTTGAAGGAAACCGAGTCATGCTCTTTAGAACTGCAGTTGCTTTAATGGAGCTATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT