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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcatttttttttcttcttcctcttgtgataaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg...

Basic information

species Glycine max
transcript GLYMA08G40200.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 5'ss of exon 4
AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcatt------tttttttcttcttcctcttgtg-ataaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg
 |||||||||||||| |||||||| ||||| ||  | |||| ||  ||| | |||||||| |||||||| ||||||||||| || ||||  |||||||||||   ||      || || |    |  ||  |||     | |||| |  | ||      || || ||   | ||   ||     |||  || || || ||| |    
GGATAGCTATGCATCCTATATTGGGCACTATCCAATGCTGGCATATTTTTCCATTGCTGAGAATGAATCAATTGGAAGAGAGCGTTACAATTTTATGCAGgtatgttaaaagcttattataacatgtcttctgtacggtagttgaaaattatgttggactt-atctggtttattaatattgatgtag--aactg-ctcctaaaa---

upper sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G14342.1 (Arabidopsis thaliana), 5'ss of exon 3
AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcatttttttttct-tcttcctcttgtga-----taaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg
 ||||| ||||| ||||| ||||| ||||||||| | ||   || ||||||||||||||| || || ||||||||| ||||||||||||  || |||||||||    |  |||  | ||||   | | | |     |  | ||| | || | ||      ||| ||   | |     | ||  || || |||   | |        
TGATAGTTATGCTTCATACATTGGTCACTACCCTATGCTTTCATACTTTGCTATTGCTGAGAACGAGTCTATTGGACGAGAACGCTACAATTTCATGCAGgtttgcctcctttcatgtcttttgcatattactttctctagtgacaaatctacagttcaagatttggattatgattctatgtttatttgattaggtgcgt------

upper sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 5'ss of exon 3
AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcatttttttttcttcttcctcttgtgataaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg-
 |||||||||||||||||| |||| |||||||| |||||||  |  ||||||||||||||||| ||||| ||||||||||| |||||||  ||||||||||||   | | | |  || |     ||||  |  | |  |   |     |  | |    ||  |   ||       |  | ||||         | ||||  
TGATAGCTATGCATCATATGTTGGCCACTACCCCTTACTGGCGTATTTTGCTATTGCTGAAAACGAATCAATTGGAAGAGAGCGCTACAATTTTATGCAGgtttgctctatgta-ttatagtagttgtattgcagttttctttaaaattgttgtttaatgaacaaattgagaaaaggaatttaaggtatgatcatatttac

upper sequence: GLYMA08G40200.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S215_103V6.1 (Physcomitrella patens), 5'ss of exon 3
AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgtt--catttttttttcttcttcctcttgtgataaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg----------------------------------------------------------
 || || ||||| || ||||| || ||    ||  |  |||  ||||||||  |||||||||||||||| |||||| |||  |||||||  |||||||||||   || | ||  | ||   |  |    || || | | ||   |  |    | |  || ||  | |  ||||  ||  |  || || ||  | || ||                                                             
GGACAGTTATGCCTCCTATATCGGGCATGCACCACTGTTGGCCTTCTTTGCAGTTGCTGAAAATGAATCCATTGGACGAGTGCGCTACAATTTTATGCAGgtgaacaatcttaatgctgtatgttacattgctagagtcatttgtaagt---cctgaatttgaacagggtccacttgcgtttttgatggttctttatatactccaagctgttcttggatcatcttgatattcacctcatctcgttcttgtgtgacttcag

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|14196138|gb|BE820012.2|BE820012
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|120496264|gb|EH224431.1|EH224431
EST:     CTATTGC--AAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|208317217|gb|GE111896.1|GE111896
EST:     GCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: GCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|209726748|gb|BW672475.1|BW672475
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|151399159|gb|EV269030.1|EV269030
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGCTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|13563498|gb|BG551718.1|BG551718
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|15816158|gb|BI788433.1|BI788433
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|193628535|gb|FK575847.1|FK575847
EST:     TTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: TTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|20449451|gb|BQ253575.1|BQ253575
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|7234170|gb|AW569510.1|AW569510
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|120529548|gb|EH257682.1|EH257682
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|27423463|gb|CA934983.1|CA934983
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|38192832|gb|CF922038.1|CF922038
EST:     CTATTACTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|120529853|gb|EH257987.1|EH257987
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|208297831|gb|GE090974.1|GE090974
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAA
EST: gi|208286390|gb|GE087806.1|GE087806
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAG
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAG
EST: gi|58018538|gb|CX705280.1|CX705280
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|208250807|gb|GE043798.1|GE043798
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGA
EST: gi|120533322|gb|EH261455.1|EH261455
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|9259379|gb|BE347526.1|BE347526
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|209703683|gb|BW670673.1|BW670673
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|6746775|gb|AW317231.1|AW317231
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAC                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
EST: gi|213601870|gb|DB980222.1|DB980222
EST:     CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAG                         AAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA
genomic: CTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcattttt ... ttttgtgcagAAAATGCTCCTGCCTTGTGGTTTGCCTCCCGAAAGAGAAGAAGATTAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATAGCTATGCATCATATATTGGACACTACCCTTTACTGGGATTCTTTGCTATTGCTGAAAATGAATCTATTGGAAGAGAACGCTACAGCTTTATGCAGgttcatttttttttcttcttcctcttgtgataaattgatagatgtgcatactttgatgtgtgctgtttccatctggctagttaattgtcttctacatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcctc