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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctccattatattgttgtgatggttcttcttttcaatctgaaacattgatggcattgtctttgttttttcttttttctttttcaatatctggcag

Basic information

species Glycine max
transcript GLYMA03G01880.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G01880.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv15s0048g01980.t01 (Vitis vinifera), 5'ss of exon 3
TGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctccattatattgttgtgatggttcttcttttcaatctgaaacattgatggcattgtctttgttttttcttttttctttttcaatatctggcag
||||||||| |   |||| |  || || ||||| || ||||||||||| || ||||| || ||||||||||||||||  ||||| ||  ||||| | ||||||     || |||  | |||| |     | ||| |    | |        |  ||||  |  |  ||| ||| |  ||      |||||     ||||||
TGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgca-----tctattg-agtgtttt-----tccttttcaatagttgtttttctctatggtttcatgattgctttctaattgaatgctttca---cttggcag

upper sequence: GLYMA03G01880.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S311_49V6.1 (Physcomitrella patens), 5'ss of exon 3
TGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctccattatattgttgtgatggttcttcttttcaatctgaaacattgatggcattgtctttgttttttct----tttttctttttcaatatctggcag-
|||  |||||||  |||||   || ||||  || |||||||||||||||||||||||||| ||||| || |||||| |||| ||  |||| ||| | |||| |   |  | |||    | || ||||  || ||  | | ||| |    ||  ||   || | | || ||     ||    ||| |         ||| |  ||  
TGAGTTGGGAAGCAACTATTCAGATGTAACAGCTCCTCAAGATGTTGCAACATATGGAGGTCTTTGCGCTCTTGCATCATTCGACAGGGCTGAGCTTAAGgtagagttccaatt----tcttttgataatt-ttaatgtgaattttggccag-gaccacagtatgttggtgacaactaaaatttctagaacgggttatgttccatt

upper sequence: GLYMA03G01880.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S31_338V6.1 (Physcomitrella patens), 5'ss of exon 3
TGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGg--------caagctctccattatattgttgtgatggttcttcttttcaatctgaaacattgatggcattgtctttgttttttcttttttcttt---ttcaatatctggcag----------------------------
 ||  |||| ||  ||||    || || || || || ||||||||||||||||||||||| ||||| || |||||| | |||||  | || ||  | || |        ||| | |||  |||  |  || |  | ||  |  || |   |   ||||  || |  | | |  ||| |  |   ||  |    |   || |||   |   |                             
CGAGTTGGGTAGCAACTACTCAGATGTTATAGCTCCCCAAGATGTTGCAACATATGGAGGTCTTTGCGCGCTTGCATCGTTTGACAGAGCGGAACTTAAAgtaaaataccaaaccctcttttaattattttttttagtgatctttctggcttataaactctgctatcgtagcttttatcatgagttagtaagatggatttaattcattttaatcatgtccaatctgtcgccaattggtag

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|57574802|gb|CX547777.1|CX547777
EST:     CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAG                         AGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
genomic: CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctc ... tatctggcagAGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
EST: gi|37997756|gb|CF809345.1|CF809345
EST:     CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAG                         AGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
genomic: CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctc ... tatctggcagAGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
EST: gi|298172715|gb|HO019755.1|HO019755
EST:     CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAG                         AGTAAAGTTGTAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
genomic: CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctc ... tatctggcagAGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
EST: gi|151408473|gb|EV278281.1|EV278281
EST:     CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAG                         AGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
genomic: CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctc ... tatctggcagAGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
EST: gi|58015910|gb|CX702652.1|CX702652
EST:     CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAG                         AGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT
genomic: CATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctc ... tatctggcagAGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTGATCGGGCAGAGTTAAAGgcaagctctccattatattgttgtgatggttcttcttttcaatctgaaacattgatggcattgtctttgttttttcttttttctttttcaatatctggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA