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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGAgtaagtctccaatttatctttccatagatatttgaaactgtctattttttagtgtctccaaagaatgttccaaagtaacttttgtcatcatttccccattctgatgatttgtttttctgaatgtcctgcag

Basic information

species Glycine max
transcript GLYMA06G22410.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G22410.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os05g32110.3 (Oryza sativa), 5'ss of exon 2
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAA---AACAGAACCTGGCAGCTGTGTAGAgtaagtctccaattt----atctttccatagatatttgaaactgtctattttttagtgtctccaaagaatgttccaaagtaacttttgtcatcatttccccattctgatgatttgtttttctgaatgtcctgcag
   |||| || |||||||| || |||||||||||| | || ||||||||||| ||| | ||||| |||| ||||||    |||   ||||| ||||||||| ||| |||    ||       |   || | | | |  |||     | | |  ||||     || |||| | || |    |  || ||   |   ||||||| ||                                 
---GTGTATCTCTCTCATCATTTTATAATGACACAATTGTGAACTGCCCAACATGCTCTTGTGGCTGCCAAAACAATGGGACAAGTCCTGGAAGCTGTGTAAAgtgagttaataaaaccaaaactcttacttcgcttcttgttgaggcccaactttt-----ctgcaaa-attgct----aacaagttccatg--catttccacag--------------------------------

upper sequence: GLYMA06G22410.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 5'ss of exon 4
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAAAACAG---AACCTGGCAGCTGTGTAGAgtaagtctccaatttatctttccatagatatttgaaactgtctattttttagtgtctccaaagaatgttccaaagtaacttttgtcat-catttccccattctgatgatttgtttttctgaatgtcctgcag
   |||| || |||||||| ||||| ||||||||| | |||  ||||||||| ||||||||||||||||  ||||| |      | || || |||||||||||||||||     ||| | |      |  |||||    ||| | | |||        ||||  ||  |||  |  | ||  |||  | || |  ||     |  |  | | || |||| |    ||   | |||
---GTGTCTCGCTCTCATCTTTCTACAATGACACAATTGTACCCTGCCCAACATGCACCTGTGGTTGCCAGAACAACATTACTCAGCCAGGGAGCTGTGTAGAgtaagttc---attcagcca--agtcaatatt----actttttgtttga-gcctcctcctgagtttgtagctgaatatttttatttatacccttttatttaattttaaattcttttccattctggtttacag
















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|8827566|gb|BE211296.1|BE211296
EST:     ACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGA                         TCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
genomic: ACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGAgtaagtctcc ... tgtcctgcagTCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
EST: gi|19052834|gb|BM731501.1|BM731501
EST:     ACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGA                         TCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
genomic: ACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGAgtaagtctcc ... tgtcctgcagTCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
EST: gi|193590089|gb|FK544781.1|FK544781
EST:     AACCTGGCAGCTGTGTAGA                         TCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
genomic: AACCTGGCAGCTGTGTAGAgtaagtctcc ... tgtcctgcagTCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
EST: gi|7925487|gb|AW831513.1|AW831513
EST:     ACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGA                         TGCAAATTCGCCACATTTAGCTCCAGTTGTATCAGCATCAGGCAAAACGGC
genomic: ACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGAgtaagtctcc ... tgtcctgcagTCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
EST: gi|11413760|gb|BF425771.1|BF425771
EST:     TGGCAGCTGTGTAGA                         TCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC
genomic: TGGCAGCTGTGTAGAgtaagtctcc ... tgtcctgcagTCCAAATTCGCCACATTTAGCTTCAGTTGTATCAGCATCAGGCAAAACGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGTGTTTCCCTCTCATCCTTCTATAATGACACAGTAGTAAACTGCCCAACCTGCACCTGTGGTTGCCGAAACAAAACAGAACCTGGCAGCTGTGTAGAgtaagtctccaatttatctttccatagatatttgaaactgtctattttttagtgtctccaaagaatgttccaaagtaacttttgtcatcatttccccattctgatgatttgtttttctgaatgtcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG