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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaagttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT

Basic information

species Glycine max
transcript GLYMA03G24280.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g03540.1 (Oryza sativa), 3'ss of exon 3
gctatagaaaa-attgtcacaactaa-ggttcattatttacttaaaatatc---caacatccaaattaagttgagtttaatcattatctgcatctactg-tttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
     |||| | ||||||  |  |     ||  ||    ||||    |||    || ||  |    ||   ||     ||  |  |   |||| | ||| |||||| | ||||| |||||||| || ||||| || |||||||| ||| | ||||||||||| ||||| || ||||| ||||  ||||| || |||||  | ||  
-----agaatatattgtcgaagttctcaatttgttgaagacttgtgttatggcacagcactctggctagcatgt-caaaactaacaaaagcatttcctgctttcagTCTCAAGGCCGTGAATCTATAGCTGCAAAACTTGTAGCTAATATGATTACAGAAGCTGGTGCGAACCGTGTCCTTGTATGTGATCTTCATTCCAGTCAAG

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G44530.2 (Arabidopsis thaliana), 3'ss of exon 3
gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaag-----ttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
     ||   | |||     |   |   || | |||    |    |  |  |  | | | || ||     || | || | || ||   || |  || | || ||||| |||||||||||||| ||||| ||||||||||| || ||||| |||||| |  | |||||| | ||||| ||||||||||| || || || || ||||
----aagctgatttgggtttatcgattgtc-tcattcctctggcttcacttagtttctagttgagagtttttcatttgactctttcgttgtacatattcttgcagACTCAAGGACGTGAATCTATTGCAGCCAAGCTTGTGGCCAATTTGATTACACAGTCTGGTGCAGACCGTGTCCTTGCTTGTGATCTTCACTCCGGACAGT

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0021g00460.t01 (Vitis vinifera), 3'ss of exon 3
gctatagaaaaattgtcacaacta--aggttcattatttacttaa---aatatccaacatccaaattaagttgagtttaatcattatctgcatctactgttt-cagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
 ||| |   || |  |   |   |  || |||||      | |||   ||| |   |  | |   | ||    |    ||| || || || | ||||||||| ||||| ||||| || ||||| || |||||||| ||||| |||||| | ||||||||||| |||||||| || || ||||||||||| || |||||||||||||
-ctaaattgaattcattttattcattagcttcatctggaccctaatgcaatgttatattttcctgtgaaaaaaa----aattataatttgga-ctactgttttcagACTCAAGGGCGAGAATCAATCGCTGCCAAACTTGTTGCAAATCTCATTACAGAAGCGGGTGCAAACCGAGTTCTTGCTTGTGATCTTCATTCTGGGCAGT

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S42_193V6.4 (Physcomitrella patens), 3'ss of exon 3
gctatagaaaaattgtcacaactaaggtt--cattatttacttaaaatatccaacatccaaat-taagttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
   |||  |  |  |    || | | |    ||| |      | |  |  |   |||   | | || |  |    | || || |      |         |||||||||||||| ||||| |||||||||||||| || ||||||||||| || || || || || ||| | || || |||||||| || ||||| |||||||
---atattagcaagggtggaagtgatgccagcataacggcgattacttcactgccattttattctatgcagcaccttatgataagacctgttctggtgcacagACCCAAGGACGAGAATCTATTGCTGCCAAGCTAGTTGCAAATTTAATCACTGAGGCTGGAGCCAATAGAGTGCTGGCTTGTGATCTTCATTCAGGGCAGT

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ35181 (Selaginella moellendorffii), 3'ss of exon 3
gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaagttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
                                       |    |  |    ||||  | ||   ||  | |     |      ||   | || || ||||| |  || || || || |||||||| ||||||||||| ||  | || || || ||||||||||||||||| ||||| |||||||| || ||||| ||  
--------------------------------------gtagcgaagtttctcatcttagttttcttcggatgttctaacgctggcgaattct-ttccagACTCTTGGTCGAGAGTCGATTGCTGCAAAGCTTGTAGCGAACCTTATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGACCTTCACTCTGGACAAA

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12994 (Selaginella moellendorffii), 3'ss of exon 2
gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaagttgagtttaatcattatct-gcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
                                           | |  |    |||||  ||   ||   || ||||   |  | |  |    | |||||||| |||||||||||||| ||||| || ||||||||||||||| |  | |||||||| ||||| || ||||| ||||| || ||| | || || |||||| 
-----------------------------------------gtagtcactgtgatccagctt---tttctttcaatctacacgtcgtgtgatgtttttcagACTCAAGGACGTGAATCGATTGCAGCAAAGCTTGTAGCAAATCTTTTGACAGAAGCCGGTGCGAACCGTGTTCTTGCATGCGACTTACACTCGGGGCAGG

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ24123 (Selaginella moellendorffii), 3'ss of exon 3
gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaagttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
                                       |    |  |    ||||  | ||   ||  | |     |      ||   | || || ||||| |  || || || || |||||||| ||||||||||| ||  | || || || ||||||||||||||||| ||||| ||||| || || ||||| ||  
--------------------------------------gtagcgaagtttctcatcttagttttcttcggatgttctaacgctggcgatttct-ttccagACTCTTGGTCGAGAGTCGATTGCTGCAAAGCTTGTAGCGAACCTTATAACTGAGGCAGGTGCAAATCGTGTTCTTGCGTGTGATCTTCACTCTGGACAAA

upper sequence: GLYMA03G24280.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ14005 (Selaginella moellendorffii), 3'ss of exon 2
gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaagttgagtttaatcattatct-gcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
                                           | |  |    |||||  ||   ||   || ||||   |  | |  |    | |||||||| |||||||||||||| ||||| || |||||||| |||||| |  | |||||||| ||||| || ||||| ||||| || ||| | || || |||||| 
-----------------------------------------gtagtcactgtgatccagctt---tttctttcaatctacacgtcgtgtgatgtttttcagACTCAAGGACGTGAATCGATTGCAGCAAAGCTTGTTGCAAATCTTTTGACAGAAGCCGGTGCGAACCGTGTTCTTGCATGCGACTTACACTCGGGGCAGG

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|254341396|gb|GR855124.1|GR855124
EST:     ATATTACTGCTGTCATTCCATATTTTGGATATGCCAGAGCTGATAGAAAG                         ACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACA
genomic: ATATTACTGCTGTCATTCCATATTTTGGATATGCCAGAGCTGATAGAAAGgtctgtttgt ... actgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACA
EST: gi|11413392|gb|BF425403.1|BF425403
EST:     ATATTACTGCTGGCATTCCATATAGTGGATGTGCCAGAGCTGATAGAAAA                         ACCCAAGGA-GTGAATCCATTGCTGGCAAGCTTG
genomic: ATATTACTGCTGTCATTCCATATTTTGGATATGCCAGAGCTGATAGAAAGgtctgtttgt ... actgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTG
EST: gi|6566864|gb|AW234496.1|AW234496
EST:     ATATTACTGCTGTCATTCCATATTTTGGATATGCCAGAGCTGATAGAAAG                         ACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACA
genomic: ATATTACTGCTGTCATTCCATATTTTGGATATGCCAGAGCTGATAGAAAGgtctgtttgt ... actgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccaacatccaaattaagttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT
                        gtttaat  putative branch site (score: 4)
                                              ctgtttc  putative PPT
                       agtttaatcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctatagaaaaattgtcacaactaaggttcattatttacttaaaatatccaacatccaaattaagttgagtttaatcattatctgcatctactgtttcagACCCAAGGACGTGAATCCATTGCTGCCAAGCTTGTAGCAAATTTAATTACAGAAGCAGGTGCAAATCGTGTACTTGCTTGTGACCTCCATTCTGGGCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC