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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

taattgacataaaatgtttttttttttctttcaaaaaatgaagtccattttgactattataaatattgatgataaaattgtcacataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGCTACCAATAGTTGGAAATGCAGCTGAACATGCAGGAGCAATCATATTTGC

Basic information

species Glycine max
transcript GLYMA18G43000.1
intron # 6
splice site 3'
intron type U2

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|193645888|gb|FK593873.1|FK593873
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|207788083|gb|GD760173.1|GD760173
EST:     ACTTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: AC-TGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|15001206|gb|BI322020.1|BI322020
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|120530398|gb|EH258531.1|EH258531
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|5126723|gb|AI748459.1|AI748459
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|208069183|gb|GD870001.1|GD870001
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGACATAATCTTG
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAG-CATAATCTTG
EST: gi|6094836|gb|AW119450.1|AW119450
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|26047871|gb|CA784524.1|CA784524
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTC
EST: gi|208035463|gb|GD832517.1|GD832517
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|5760718|gb|AI966081.1|AI966081
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATAGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATTATCTTG
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTG
EST: gi|26048877|gb|CA785330.1|CA785330
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|193525030|gb|FK482831.1|FK482831
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|193462335|gb|FK426834.1|FK426834
EST:     TGTGGTGGATACAATTGAGG                         ATGCATCAGATTC-TGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: TGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|6913524|gb|AW395054.1|AW395054
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|208166460|gb|GD965526.1|GD965526
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|207717379|gb|GD699848.1|GD699848
EST:     TGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: TGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|193382197|gb|FK347998.1|FK347998
EST:     GACTGTGTTCATAGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTG
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTG
EST: gi|6952300|gb|AW424368.1|AW424368
EST:     GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: GACTGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
EST: gi|208206484|gb|GE007931.1|GE007931
EST:     TGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGG                         ATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC
genomic: TGTGTTCATTGCTGTGTTGTCTGAATATGTGGTGGATACAATTGAGGtaattgacat ... acataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaagtccattttgactattataaatattgatgataaaattgtcacataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGCTACCAATAGTTGGAAATGCAGCTGAACATGCAGGAGCAATCATATTTGC
                          tattgat  putative branch site (score: 3)
         attttgactattataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattgacataaaatgtttttttttttctttcaaaaaatgaagtccattttgactattataaatattgatgataaaattgtcacataacaggATGCATCAGATTCGTGGGGTTTGTCTGTGAGCTTTCTCAGCATAATCTTGCTACCAATAGTTGGAAATGCAGCTGAACATGCAGGAGCAATCATATTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA