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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca...

Basic information

species Glycine max
transcript GLYMA14G01530.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca-
 || ||||| |||||||||||| | || ||| | || |||||||| ||||||||||||||||| || ||  |  | ||| | ||||| ||  | || || ||||  ||| | |  |   |||  ||   ||     ||    |  ||           ||    |||||   |    || | || |     |   | ||| 
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaat-tttctttaaacttttgcaagttcttgaatatttgaatcattctcagttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat

upper sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S258_52V6.1 (Physcomitrella patens), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgattac---gtccttactgcggtcgttctttatttcatgtttattgctcaaacaca
 |||||||| || ||||| ||| | || ||| | || ||||||||||||||||||||||||||||| || || || || || ||||||||| | ||||| |||||  |  ||  | |         ||  | |  | | ||| |   ||||     | ||   ||      ||  | |       | || ||| |      ||
CTTTCAGGCGGAAATCAATCAGTTGCTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTGCGAGAACTTATCAGCAATTCTTCTGATgtaag--tgctagtgctgacgaaagtcccatgcggtcttcttgtcgggattgtagtggccagtctatctgtgtcatgtgcacgccgattcttggttgg-tgca

upper sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgat---tacgtccttactgcggtcgttcttta--tttcatgtttattgctcaaacaca--
 || ||||| |||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||  | || |||||||||||||||||||| || || ||  ||  ||      | |      ||||     |  | |  | |||   | | | ||| ||||| |   ||       ||    ||  ||   | |   |   
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatattttactgctattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcattctttctgcgatttccag

upper sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ29061 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca
 || ||||| |||||||||||||| |||||||| || |||||||| |||||||||||||||||||| ||  | || |||||||||||||||||||| || || ||  |||   |  ||||||||   |   |   | ||    | ||  ||     | | |||||  || | |  | | ||                   
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcc--tccttgttcttccagttcttgtcaaactctttcttcttctcatgctgcg-ccgctgtg-actccag------------------

upper sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttat---cgatccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttcttta--tttcatgtttattgctcaaacaca--
 || ||||| |||||||||||||| |||||||| || ||||||||||||||||||||||||||||||||  | || |||||||||||||||||||| || || ||  ||  ||   || ||   | ||      |    |||   | | |  || | | ||| ||||| |   ||       ||   |||  ||   | |   |   
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatatttcactgcgattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcgttctttctgcgatttccag

upper sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcg-atccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca
 || ||||| |||||||||||||| |||||||| || |||||||| |||||||||||||||||||| ||  | || |||||||||||||||||||| || || ||  |||   |   | |||      ||| || |  || || |  |  | | | |    |||| ||   ||                            
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatg-ctgcgctgctgtgactccag-------------------------

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|213618380|gb|DB969378.1|DB969378
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213587990|gb|DB957449.1|DB957449
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213597843|gb|DB962196.1|DB962196
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGA-AAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|209700012|gb|BW652924.1|BW652924
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213613889|gb|DB960910.1|DB960910
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|18041089|gb|BM309383.1|BM309383
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|6501961|gb|AW203334.1|AW203334
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|11274820|gb|BF325146.1|BF325146
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|209723071|gb|BW662447.1|BW662447
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|6667546|gb|AW278997.1|AW278997
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|213598667|gb|DB964261.1|DB964261
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
EST: gi|17024084|gb|BM095118.1|BM095118
EST:     ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGAC                         GCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT
genomic: ACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttt ... aacaatgtagGCTTTGGACAAGATTCGATTTGAGAGTCTTACAGACAAGAGCAAGCTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcgatccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA