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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG

Basic information

species Glycine max
transcript GLYMA20G18980.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G848768_T02 (Zea mays), 3'ss of exon 4
----------------------------gtatgtt---tagaatttagata--gattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatc-cagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
                            | ||| |   ||  ||  |||    |||  |   |           | |  |   | | |  | ||  || |   ||||| | || |  |  ||||||| || |||||||| ||||| ||  | || |||||||||||||| ||||| || |||||||| || |||||||||| |||||| | ||||||||| |
gtaactgataactgttgtttacgatcatgcatgctacctaatatgaagaagacgatcctatcttctggtggacaaaaaaagaagagataatgatgcat-cccatgatgatgttgttgttgcagAAACCGTCCCTGTTAGAACTGTCAACCGCCAGTGTTCATCTGGGCTACAGGCAGTAGCTGATGTCGCAGCTGCTATAAAGGCTGGTTACTATGACATAG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G33150.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatt----tatacttgtgatgttattttcatc--cagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
||||||||     ||  ||  |  || |     ||  || |  |   |||  |||| |  ||    ||| ||  |  |||||| |||||   ||||||| ||| |||| || ||||| ||||| || || ||||||||||| |||||||||||||||||||| ||||| || |  || || || ||||||||||
gtatgttt----cttctatgtacagtacaatacaa--tggtgaaaagtctttgtttttatttcctgtatgctcatcctgttatgttcatttgcagAAACCGTGGCTGTCAGAACTGTGAATAGACAGTGCTCATCTGGGCTTCAGGCTGTTGCTGATGTAGCCGCTGCCATTAAAGCGGGATTTTATGACATTG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G04710.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatcc---agAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
|||   ||    | |  ||  || ||  | ||||| ||  | | |  | |  ||||||| |  || ||| || | || || ||       ||||||||| ||  | || || || || || || |||||||||||||| ||||||||||||||||| || ||||| ||||  ||||| || ||||||||||
gtaatattttcttctgtatt-atggtaatcctgaatcttttct-tctttttcgtttgttgt--atgcttatgctctttttgtctgttggaagAAACTGTTCCCATCAGAACCGTGAACAGACAGTGTTCATCTGGGCTTCAGGCTGTTGCTGATGTTGCCGCTGCCATAAAAGCTGGTTTTTATGACATTG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0051g00720.t01 (Vitis vinifera), 3'ss of exon 4
gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
           ||||   |  | | | |||   |   |    | ||  |    ||  || || | |  | | || |  | |   | |||||||||||||||| || ||||| || ||||||||||||||||| || ||||| |||||||||||||||||||| || |  |||||||| ||||||||||
-------gtatatttccttgaactatcctttatatttttggttttgtacccatttcattgttcacaaatattatatc-tgtgatttcagAAACTGTGCCTGTCAGAACTGTGAACAGGCAATGTTCATCTGGTCTTCAGGCAGTTGCTGATGTAGCTGCTGCAATTAAAGCTGGGTTTTATGACATTG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S55_275V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------------------gtatgtttagaatt--tagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG-
                                                                                                                 || | |||    ||  |   |  | ||   || |||||   || |  ||| |||  || | ||   | |||  | |||       |  ||||||||||||| ||||| ||||| || |||||||| |||||||| || || |||||||| |||||||| || ||||| |  || || |||||||| |||| 
gtgagcttatagctatgtttcttatggccatatatgtaatgccgctcaggaagatagttgtctttttcatgggagtgtttaatgcgcaggtgactaataatttagggaaatatgtctattttatgttgtttattgaaatgcctttatgaactccat-tgagatttgg-cttctgataagttcttccg-tgtggcggcaa--cagAAACTGTGCCCGTTAGAACTGTGAACAGGCAATGCTCATCTGGACTGCAAGCTGTTGCGGATGTAGCGGCAGCTATTAAAGCAGGTTTCTATGATATTGG

upper sequence: GLYMA20G18980.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35624 (Selaginella moellendorffii), 3'ss of exon 4
gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtga-----tgttattttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
                  |  ||  |  ||||     |  ||||| |  |  |||| |  || |   ||| ||     | |||| |      |||||||||||||||| | || || || ||||||||||| ||||| ||||| || || |||||||| |  |||||||| | ||| || |||||||| ||||
-----------------gtttatgatttttctttgttttctatataactt--gtttttctttcaccattgagactaacttttatgtcttggtagAAACTGTGCCTGTTCGTACCGTGAACAGGCAATGTTCTTCTGGCCTCCAAGCAGTAGCTGATGTTGTGGCTGCTATCAAGGCCGGATTCTATGATATTG

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|213612208|gb|DB956889.1|DB956889
EST:     TCANAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|254331905|gb|GR843648.1|GR843648
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|193665725|gb|FK609640.1|FK609640
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGACCTGTTAGGACTGTTA
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTG-CCTGTTAGGACTGTTA
EST: gi|254337494|gb|GR845171.1|GR845171
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|308099050|gb|HO760891.1|HO760891
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|51345318|gb|CO986051.1|CO986051
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|151407628|gb|EV277443.1|EV277443
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|254319376|gb|GR828996.1|GR828996
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|21994717|gb|BQ786245.1|BQ786245
EST:     TCAAAGAGCTAGAGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGCTAATAGGCAATGGTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
EST: gi|9986215|gb|BE660323.1|BE660323
EST:     TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTG                         AAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG
genomic: TCAAAGAGCTAGTGAATGCCGAATGGCTGCATTTTATGCTGGTTTTCCTGgtatgtttag ... tttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgatatatgatctgggtttgttatttatacttgtgatgttattttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG
 acctgat  putative branch site (score: 4)
                                            ttttcatcc  putative PPT
                   tttgttatttatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttagaatttagatagattgtgcttctgaacctgatatatgatctgggtttgttatttatacttgtgatgttattttcatccagAAACTGTGCCTGTTAGGACTGTTAATAGGCAATGTTCATCTGGGCTCCAGGCTGTTGCTGATGTAGCTGCTGCTATAAGGGCTGGGTTCTATGACATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT