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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTGGTGTTCAATCAAAGAGCATAAGTAATGACACCCTAGCAAGGCTGGCTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatttagaagatttcttctccttaatttttatttatgcaatagttgttaactgtataagctctcaaatgttaggaattttaatatactgtggtt...

Basic information

species Glycine max
transcript GLYMA14G02180.4
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02180.4 (Glycine max), 5'ss of exon 5
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 5'ss of exon 5
TACTGGTGTTCAATCAAAGAGCATAAGTAATGACACCCTAGCAAGGCTGGCTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcat--ttagaagatttcttctccttaatttttatttatgcaat---agttgttaac-tgtataagctctcaaatgttaggaattttaatatactgtggtt--------------------------------------------------------
 | |||||||||| | |||||||| || ||||| || || |||||| |||||||||| ||||| || || |||||||||||||  || || ||  | ||||| |  ||   | |     ||| |  ||  | |  |    ||   || |    | ||   |  |||  ||   ||      |||       | | |   |||   |                                                        
AAATGGTGTTCAAACCAAGAGCATTAGCAATGAAACACTTGCAAGGTTGGCTAAGACTGTCTTGACTCTTAAAGAAGATAAAATGCAAAGACTTAAGAAGgttagtcaaaatcatggtctttgtgatctctgacatgagcttggtcagtttaggctgcacatatgttgaaatcctttctgattaattgcgctgaaagtttgtaacttttctctgcaccattcttgtttgtggatttcattaatgtatcttggttttatgcag

upper sequence: GLYMA14G02180.4 (Glycine max), 5'ss of exon 5
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 5'ss of exon 4
TACTGGTGTTCAATCAAAGAGCATAAGTAATGACACCCTAGCAAGGCTGGCTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatttagaagatttcttctccttaatttttatttatgcaatagttgttaactgtataagctctcaaatgttaggaattttaatatactgtggtt--
 |||||||| ||||| || ||||| || |||||||||||  | |||||||||||||| |||||| | || || ||||| || || |||||||| || |||||||    |||||      |  | | | |  ||  ||||     || ||||  |   |   | | |  |      ||  || |||| ||| |  |  | |  
AACTGGTGTGCAATCCAAAAGCATTAGCAATGACACCCTTTCTAGGCTGGCTAAGACAGTCTTAGCACTAAAGGAAGACAAGAAGCAGAGGCTACAGAAGgtaaaatttttagtgttcctgctttacctggttagtattgtgcgaagagttaatcggtagttcatcattttgc--tttagatttttcatacatggatgctct
















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|7147025|gb|AW508947.1|AW508947
EST:     CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
genomic: CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
EST: gi|38193636|gb|CF922842.1|CF922842
EST:     CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
genomic: CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
EST: gi|192314484|gb|FK008426.1|FK008426
EST:     CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
genomic: CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
EST: gi|207712616|gb|GD694528.1|GD694528
EST:     CGCTG-AAGAAGNT-AAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTAATTGATCTTTGGAATCTAATGGATACT
genomic: CGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
EST: gi|5058140|gb|AI736616.1|AI736616
EST:     AGAAGATAAAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTAATTGATCTTTGGAATCTAATGGATACT
genomic: AGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
EST: gi|192314483|gb|FK008425.1|FK008425
EST:     CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
genomic: CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
EST: gi|207690818|gb|GD673702.1|GD673702
EST:     CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAG                         CTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT
genomic: CTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatt ... tatcatgcagCTCCAAGAATTAGCTTCTCAGTTGATTGATCTTTGGAATCTAATGGATACT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTGGTGTTCAATCAAAGAGCATAAGTAATGACACCCTAGCAAGGCTGGCTAAGACCGTCTTAACGCTGAAAGAAGATAAAAAACAGAGGCTGCACAAGgtaatgcatttagaagatttcttctccttaatttttatttatgcaatagttgttaactgtataagctctcaaatgttaggaattttaatatactgtggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttctcc