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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggtttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG

Basic information

species Glycine max
transcript GLYMA07G01260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
-----attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggttt----aatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
      |  | || ||| | | ||||| ||||     |  || | |   |  |  ||   |  ||  | |   | | |||||        |||   ||      | ||||||||||  || ||||||||||||||||||| |||   |||||||| || || || |||||||||||||| |||||  ||| ||| |||||||| || ||
accttctgaactacattcttt-attattttgc-----tcttttttaatcttggacatcttacattctata---tttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacat--------gtttcaaac---agtgtactgatt--tttcggccttggtttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                    ||    || |   | ||||||  ||     |  |||  |     ||||   |  |||        |||| |        | |||  | |  | | |      | ||    |||| |||||  |||||||  |||  || ||||| ||||||||||||||||| || |||||||| || ||||| |||||| ||||||| |||||||| || ||
gtaaactcttgaatttggcaatcatgtagagcttgtgattagtttcacttacatgtcttagatgtatgatgtagcatatatgcctgttttatttttggatatacctactgatatagtttcctgattggctcagATTATGTTTTGGAAGAGGTTAAGAAGGCTGGTTTTACTGAACCTACGCCTATACAATCTCAGGGGTGGCCAATGGCTATGAAGGGACGTGATCTTATCGG

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
-attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggttt----aatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
 | | | |  | ||      | |||||  || ||     |  ||| ||||    | || ||  ||     ||  | ||| ||      |   ||    | |||||||||||| ||| ||||||||||||||||||||||| |||||||||| ||||| ||| ||||||| ||||| |||||||||||||| |||||| | || ||
aaatcagtg-actggcaacctttcttgagaagttatgctttggatgatgg----atattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S59_81V6.1 (Physcomitrella patens), 3'ss of exon 3
attgattatattgtatgattatcttgca--aaatttgttatcag-attatgggat--gacatgtttcaaacagtgtactgatttttcggccttggtttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
       | | ||| |||||     | |       ||||    |    || || |  |    | |    ||  ||    | || |  |     |   |    |||| |||||  || | ||  |    || || || || || || || ||  | |||||| | ||||| ||||||||||||||||||||||| ||  |||| ||
-----ggacactgtgtgattgatcgggatcggtcctgttggtggtggcattgggtttgtggcgctgatcacgctgcggcggttgtgtgtttgggaaatggagcagATTATGTGCTGCATGAGGTGCTGAAGGCAGGGTTCACGGAGCCAACAGCTATTCAAGCGCAAGGCTGGCCCATGGCTTTGAAGGGGCGCGACTTGATCGG

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10791 (Selaginella moellendorffii), 3'ss of exon 2
attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggtttaatc--cagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                                        ||   | ||  |    | |     |||  ||  |||||  ||     ||| |   |   |||| |||||  |  | ||| ||   ||||| || || |  || || ||  |||||||| ||||||| ||||||||||||||||| ||| | |||||  ||||
--------------------------------------gtaggcgaaggtttcttctatcgaggacaaggttttgattgatcttatgtggatgttttggcagACTATGTTCTCCAGGAAGTTCTCAAAGCCGGTTTCAAGGAGCCCACCGCCATTCAAGCTCAAGGATGGCCCATGGCTTTGAAAGGGAGGGATCTAGTAGG

upper sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26152 (Selaginella moellendorffii), 3'ss of exon 2
attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggtt-taatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                                        ||   | ||  |    | |     |||  ||  |||||  ||     ||| | |  |||||| |||||  |  | ||| ||   ||||| || || |  || || ||  |||||||| ||||||| ||||||||||||||||| ||| | |||||  ||||
--------------------------------------gtaggcgaaggtttcttctatcgaggacaaggttttgattgatcttatgtggatgttttccagACTATGTTCTCCAGGAAGTTCTCAAAGCCGGTTTCAAGGAGCCCACCGCCATTCAAGCTCAAGGATGGCCCATGGCTTTGAAAGGGAGGGATCTAGTAGG

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|209699629|gb|BW655721.1|BW655721
EST:     TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAG                         AATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
genomic: TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
EST: gi|10709520|gb|BF009244.1|BF009244
EST:     TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAG                         AATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
genomic: TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
EST: gi|207713410|gb|GD695785.1|GD695785
EST:     TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAG                         AATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
genomic: TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
EST: gi|209720525|gb|BW675024.1|BW675024
EST:     TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAG                         AATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
genomic: TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
EST: gi|13479970|gb|BG509313.1|BG509313
EST:     TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAG                         AATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA
genomic: TCGAGATATCCCGAAACCTGTCAAGTCCTTTCATGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggatgacatgtttcaaacagtgtactgatttttcggccttggtttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                            tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggtttaatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - -tgtatga
- - - - - - - - - - - cttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggccttg