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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacactgaatttttgtttaattgaaataatatacaaatacaatggaggccatccatctattaacaacattctgtcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGTCAAGAGGAATGTACAAAGTCTGATGAAGAAAGTGAAGATGGGTTCTTTG

Basic information

species Glycine max
transcript GLYMA18G48000.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G48000.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G65470.1 (Arabidopsis thaliana), 3'ss of exon 7
gtacactgaatttttgtttaattgaa---ataatatacaaatacaatggaggccatccatctattaacaacattctgtcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGTC---AAGAGGAATGTACAAAGTCTGATGAAGAAAGTGAAGATGGGTTCTTTG
       | |  ||| || |||| |    ||  | |  |||    |   | |    |    || |||  | |     | ||||  |||| ||| |||||||||| ||||| |||||||| ||||||||||| ||| ||    |||| | |||| ||||| ||||||| |||  |||   ||         
-------gtaggtttattgaattcagtacatgctttttaaacttgacaaaagatcactgggtaataaagatac----ttctttacagGAAGAAGCTGGTGAAAGCCTTTCAGATTGTGAGAAAGATGAAGACGAAAGTTTGGAAGAAGGATGTTCAAAGGCTGATGATGAAGATGATAGTGAAGATG---
















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|193356533|gb|FK321846.1|FK321846
EST:     AGGATCCAAGCCTGGATTATGTTGTCAGCAGCGATGAGGAATGGGAAGAG                         GAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
genomic: AGGATCCAAGCCTGGATTATGATGTCAGCAGCGATGAGGAATGGGAAGAGgtacactgaa ... tcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
EST: gi|193698453|gb|FK639034.1|FK639034
EST:     AGGATCCAAGCCTGGATTATGATGTCAGCAGCGATGAGGAATGGGAAGAG                         GAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
genomic: AGGATCCAAGCCTGGATTATGATGTCAGCAGCGATGAGGAATGGGAAGAGgtacactgaa ... tcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
EST: gi|193488764|gb|FK453633.1|FK453633
EST:     AGGATCCAAGCCTGGATTATGATGTCAGCAGCGATGAGGAATGGGAAGAG                         GAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
genomic: AGGATCCAAGCCTGGATTATGATGTCAGCAGCGATGAGGAATGGGAAGAGgtacactgaa ... tcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
EST: gi|193419948|gb|FK385386.1|FK385386
EST:     GGATCCAAGCCTGGATTATGATGTACAGCAGCGATGAGGAATGGGAAGGG                         GAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT
genomic: GGATCCAAGCCTGGATTATGATGT-CAGCAGCGATGAGGAATGGGAAGAGgtacactgaa ... tcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatacaaatacaatggaggccatccatctattaacaacattctgtcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGTCAAGAGGAATGTACAAAGTCTGATGAAGAAAGTGAAGATGGGTTCTTTG
                             tattaac  putative branch site (score: 1)
                                      cattctgtccttttt  putative PPT
      aaatacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacactgaatttttgtttaattgaaataatatacaaatacaatggaggccatccatctattaacaacattctgtcctttttagGAGGAACCTGGTGAAAGTCTTTCTGATTGTGATAAAGATGAAGAGGAATGTCAAGAGGAATGTACAAAGTCTGATGAAGAAAGTGAAGATGGGTTCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG