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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG

Basic information

species Glycine max
transcript GLYMA05G28480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g26850.2 (Oryza sativa), 3'ss of exon 1
ggtcattgggttttg-tggatctagtggattatgaattgat-tttgctttattgctcgtgttattttttattaacct---tttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
     |    | ||  || ||   | | ||||  |  || | | |  |  | || |  | | ||||||  || |  |   ||   |||||| || |     ||||||||||||| |||| || ||||| |||||||||||||||||||| ||||||||||| ||||| ||||| ||||| ||||| || || ||    || ||||
-----tgaaatattactgaatgctgggaattacaatctgttatattttgcaatgattttatcatttttgcttgagatatattaactctgtgtttcttctgaacagTTTGACAACCTGTATGGTTGCCGCCACTCTCTCCCTGATGGTCTCATGAGGGCTACCGATGTTATGATCGCTGGCAAGGTTGCCGTGGTCTGCGGTTATG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G111909_T01 (Zea mays), 3'ss of exon 2
-ggtcattgggttttgtggatctagtggatta-tgaattgattttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
     |||   |||  |      |   | |||     ||| |    |   | | |   |  ||   || | ||   || | || | |  |  ||| | |||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||| || || || ||||||||||| ||||| || || ||   ||||||||
acaatattttttttcttcttataaacagcttagcatgttgctagaaccaaaatccaactactaagattaactatatttat-atgtttcctcctgttt-acagTTTGACAACTTGTATGGTTGCCGCCACTCCCTCCCTGATGGTCTGATGAGGGCCACAGACGTTATGATTGCTGGCAAGGTTGCCGTGGTCTGTGGATATG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G015295_T01 (Zea mays), 3'ss of exon 1
-ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgctcgtgttattttttattaacctt-ttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
     | |   |||  || |   |||     |||  ||| |  | |   | | |   | |||    | | |||  |  ||||| ||    |       ||||||||||||| |||| || ||||| ||||| ||||||||||||||||||||||| ||||| || ||||| || |||||||| || || ||    ||||| |
ttacaaatatttttcttgtaaacagtttgacatg--ttgctagtaccgaaattcaactattaagactaactaaattgattgatatggttctcctctgaacagTTTGACAACCTGTATGGTTGCCGCCACTCGCTCCCTGATGGTCTGATGAGGGCCACTGACGTTATGATCGCCGGAAAGGTTGCCGTGGTCTGCGGATACG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G13940.1 (Arabidopsis thaliana), 3'ss of exon 1
----ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
     |||| |   | |  ||  |    ||  ||   | |  |  ||   ||    ||  |||    | ||| | |    || || |||  | |||  | |||||| ||||||||||| || ||||||||||| |||||||||||||| |||||||| |||||||| ||||| ||||||||||| |||||| |   ||||||||
gaaaagtcaatatttctcatgctttctttgattttatattcaacgttttgtttacacttatgtg--ctgttactgataaattcatttgt--tcttgatttacagTTCGACAACTTGTATGGTTGCCGTCACTCACTCCCTGATGGTCTCATGAGGGCCACTGATGTCATGATCGCTGGAAAGGTTGCTGTTATCTGTGGATATG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G23810.1 (Arabidopsis thaliana), 3'ss of exon 1
--ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgct--cgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
   || | ||| |    |         | |  |    |   ||||||| | || ||    ||   || | | ||   ||  |||| |||    |||  | | ||||||||||||||||||| ||||| ||||| || || |||||||| ||||||||||||||||| ||||||||||||||||| |||||| |   ||| ||||
attgttaatggatccatttaggtggaagcaagaactctgttttttgctctgtttctgctctgcatttctctgtttcactgatgatttgt----ttgctttatagTTTGACAACTTGTACGGATGCCGACACTCGCTTCCCGATGGTCTCATGAGGGCTACTGATGTTATGATTGCTGGAAAGGTTGCTGTTATCTGTGGTTATG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0029g00330.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------------------------ggtcattgggttttgtggatctagt--ggattatgaattgatt--ttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtg---acagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
                                                || |  |||| |||||||||||  ||||||  |   || |  |   ||| |   | || || |||| | ||  | |    || |   ||| ||  ||   |||||| ||||| ||||| || ||||| || || ||||||||||| |||||||| ||||| || ||||||||||| |||||||| || |||||    ||||| |
gtattctccagatctgtgatatttgggaattgttttcaacgattcaaccaatttgtttggtggatctagtttggattactagaagagtcgtaattttgtgttttgttttgttttgt-ttttcttaacaattttctgttctggatgcaaacagTTCGACAATTTGTATGGATGCCGCCATTCACTCCCTGATGGGCTGATGAGAGCTACGGACGTGATGATTGCCGGAAAGGTTGCAGTTGTATGCGGATACG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g09840.t01 (Vitis vinifera), 3'ss of exon 1
ggtcattgggttttgtggatctagtggattatgaattgattt-tgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
  |     || | ||     |    ||| ||   || ||||| | |  |  || | |     |||| | ||    | ||  ||  |||| ||   || ||||||||||||||||| || ||||| ||||| ||||| |||||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||   ||| ||||
acttggcagggtgtggaccccggagggaatagttatggatttgttcagtgctgattgaccccttttatgttctaatatttttcaatggtattcaatg-cagTTTGACAACTTGTATGGATGCCGACACTCCCTCCCCGATGGTCTCATGAGAGCCACTGATGTCATGATTGCTGGCAAGGTTGCTGTGGTCTGTGGGTATG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S20_229V6.1 (Physcomitrella patens), 3'ss of exon 2
ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgct-cgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
         ||  |||||  |  |||  |   | ||   ||| | ||   ||     || |  | | |  |   |   |||    ||| ||  |||| ||||| |||||||||||||| ||||| ||||| || || || || |||||||| || || || ||||||||||| || ||||| |||||  |    || || |
---------gtaatgtggtcc--gtgactgtcggatacctttcgtttggatgtgatttgatggtgtgtggttggcggctgacgcttgggttgttgtg-cagTTCGACAACTTGTACGGTTGCCGCCACTCGCTGCCCGACGGCCTGATGAGAGCGACGGACGTGATGATTGCCGGGAAGGTTGCTGTGATCTTCGGGTACG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ11444 (Selaginella moellendorffii), 3'ss of exon 1
ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
                         | | |    | |  ||||| ||||||         | ||  |  | | | |  |  ||    |||  | | |||||| |||||| | ||||| ||||| ||||||||||||||||| || ||| | || |||||||||||||| ||||| ||||| || || || |||||||| |
-------------------------gtactcacgacttcttttg-tttattctcttgaaaagttagtgctcatcgtgagtgct----tttctttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGAGCAACTGATGTGATGATCGCTGGGAAGGTCGCAGTCGTCGCTGGATACG

upper sequence: GLYMA05G28480.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ11220 (Selaginella moellendorffii), 3'ss of exon 1
ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
                         | | |    | |  ||||| |||||||        | ||  |  | | |      |  ||| |||| | | |||||| |||||| | ||||| ||||| ||||||||||||||||| || ||| | || |||||||||||||| ||||| ||||| || || || |||||||| |
-------------------------gtactcacgacttcttttg-tttattgtcttgaaaagttagtgctcatc-----gtgagtgcttttcttttacagTTCGACAACCTTTACGGCTGCCGACACTCTCTCCCTGATGGACTCATGCGAGCAACTGATGTGATGATCGCTGGGAAGGTCGCAGTCGTCGCTGGATACG

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|15813390|gb|BI785665.1|BI785665
EST:     CTTTTCTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|254334445|gb|GR844230.1|GR844230
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGG-TGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|16348464|gb|BI974059.1|BI974059
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|7925987|gb|AW832013.1|AW832013
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|15815317|gb|BI787592.1|BI787592
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|192322571|gb|FK014692.1|FK014692
EST:     CAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|13791038|gb|BG653629.1|BG653629
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|7925437|gb|AW831463.1|AW831463
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
EST: gi|20498111|gb|BQ273041.1|BQ273041
EST:     CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAG                         TTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG
genomic: CTCTACTCTTCCCTGCTATTAATGTCAATGACTCTGTTACCAAGAGCAAGgtaatgtctc ... tgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG
             ttattttttattaacc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcattgggttttgtggatctagtggattatgaattgattttgctttattgctcgtgttattttttattaaccttttgatctgtggttttgtgtgacagTTTGACAACTTGTACGGGTGCCGTCACTCTCTCCCTGATGGTCTGATGAGGGCTACTGATGTGATGATTGCTGGAAAGGTGGCTGTTGTGGCTGGATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - ggttttg
- - - - - - - - - - - - - - - - - - - - - tgcttta
- - - - - - - - - - - - - - - - - - - - - - - - - -gctcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtgg