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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgtcacatttggggtttgccctttgatttgaaattttaaccttaaataacaactttggttcttgctactcattggttttttgttgtctgtgatactaacctcacttactctccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCTCTTATAGTTGCTAAATG

Basic information

species Glycine max
transcript GLYMA06G13720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13720.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0060g01920.t01 (Vitis vinifera), 3'ss of exon 2
gtgatgtcacatttggggtttgccctttgatttgaaattttaaccttaaataacaact---ttggttctt------gctactcattggttttttg-------ttgtctgtgatactaacctcacttactctccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCTCTTATAGTTGCTAAATG
  | | | ||  ||  |    ||  | |  |||   ||| || |  | ||| || |||   |   || ||        |  | ||||  || |         |||||| ||    | |   |  ||  | |  |  |||||| || || || ||||| |||||||||||| | ||||| |||||||||||||| || |||||||||||
--gttttaactctttagag--gcattcttgttttttattgtaccaatgaatgacgactgattcacttatttaaaaaaatgataattgtcttctaaaatgactttgtctatgtcttttatagcctttcattttaatggcagTACCCAGGACTCGAACCAGTTTTGGATGATTTGCTTCCGAAGAAGTCCCCTCTCATTGTTGCTAAATG
















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|207703438|gb|GD685398.1|GD685398
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATAT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATAT
EST: gi|298187707|gb|HO031664.1|HO031664
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|298164604|gb|HO014249.1|HO014249
EST:     AAGTGAAGGCATCTGTTCAGCGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|298192440|gb|HO036522.1|HO036522
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|151394068|gb|EV263939.1|EV263939
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|298169962|gb|HO018586.1|HO018586
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|193399249|gb|FK364751.1|FK364751
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|209712614|gb|BW653747.1|BW653747
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|9899350|gb|BE608318.1|BE608318
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|193412006|gb|FK380401.1|FK380401
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|254323561|gb|GR836007.1|GR836007
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|151412868|gb|EV282680.1|EV282680
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|193700872|gb|FK639939.1|FK639939
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|192300163|gb|FG989285.1|FG989285
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|208277879|gb|GE074886.1|GE074886
EST:     AGTGAAGGCATCTGTTCAAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AGTGAAGGCATCTGTTC-AACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
EST: gi|254323562|gb|GR836008.1|GR836008
EST:     AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAG                         TATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT
genomic: AAGTGAAGGCATCTGTTCAACGAAAAATACGACAAAGTATTGCTGAAGAGgtgatgtcac ... tccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactcattggttttttgttgtctgtgatactaacctcacttactctccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCTCTTATAGTTGCTAAATG
                                 cctcacttactctcc  CT-rich tract
          ttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgtcacatttggggtttgccctttgatttgaaattttaaccttaaataacaactttggttcttgctactcattggttttttgttgtctgtgatactaacctcacttactctccactgcagTATCCGGGCCTTGAACCTGTTTTGGATGATATACTTCCCAAGAAGTCCCCTCTTATAGTTGCTAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT