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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacttttacgagtgtcataagtataggtggaaaataaggatgataccatggttgattgctatgctgtggtttcaatacaatttggatgttttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGATTTGAATCTGATGAGGACTCTCCTCCAAGGAAAACAACCACCCATCGGC

Basic information

species Glycine max
transcript GLYMA06G21900.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G21900.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g07000.t01 (Vitis vinifera), 3'ss of exon 6
gtacttttacgagtgtcata-agtataggtggaaaataaggatgataccatggttgattgctatgctgtggtttcaatacaatttggatgtt-----ttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGATTTGAATCTGATGAGGACTCTCCTCCAAGGAAAACAACCACCCATCGGC---------
    ||||||     | | | ||| ||  |   || | || ||  |    || |  |     ||  | |||||  |  |||| |||  | ||     |||||||||||||||||||| |||   |||||||          ||||||  | |||||| ||||||| |||||||||||||||||||| || |   | | ||| ||||         
-ctgttttacattgataaaatagtctatatatgaattgagaatatt----tgttcaaccatcatattatggtta-ataacaaattgtgttttggaatttcttgcagGAACCAAAGCAAAAGGGTAAGGAGT---------ATGCCAAGCGCAAGGGAATTGAATCAGATGAGGACTCTCCTCCAAGAAAGAGTGCTAGCCACCGGCGAATGGCAT

upper sequence: GLYMA06G21900.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv17s0000g07160.t01 (Vitis vinifera), 3'ss of exon 10
--gtacttttacgagtgtcata-agtataggtggaaaataaggatgataccatggttgattgctatgctgtggttt-caa--tacaatttggatgttttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGATTTGAATCTGATGAGGACTCTCCTCCAAGGAAAACAACCACCCATCGGC---------
  |   ||||||     | | | ||| ||  |   || | || ||  |    || |  |     ||  | |||||  |||  | |  ||||||   ||||||||||||||||||||| |||   |||||||          ||||||  | |||||| ||||||| |||||||||||||||||||| || ||  | | ||| |||          
gtgctgttttacattgataaaatagtctatatatgaattgagaatatt----tgttcaaccatcatattatggttaacaaattgcgttttggaa--tttcttgcagGAACCAAAGCAAAAGGGTAAGGAGT---------ATGCCAAGCGCAAGGGAATTGAATCAGATGAGGACTCTCCTCCAAGAAAGACTGCTAGCCACCGGAGAATGGCAT
















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|254345263|gb|GR855813.1|GR855813
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|6455229|gb|AW185912.1|AW185912
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|193630070|gb|FK578570.1|FK578570
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|58024376|gb|CX711117.1|CX711117
EST:     ATGAAGAAGCTGATCAAGTTAATGATGCATCAGATGAGGAGGATGAGGAG                         GATCCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|254345262|gb|GR855812.1|GR855812
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|58021318|gb|CX708059.1|CX708059
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|14125052|gb|BG789490.1|BG789490
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|193637951|gb|FK586201.1|FK586201
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|58014328|gb|CX701070.1|CX701070
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|192325644|gb|FK019500.1|FK019500
EST:     ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: ATGAAGAAGCTGAACAAGTTAATGATGCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
EST: gi|193457712|gb|FK425004.1|FK425004
EST:     GCATCAGATGAGGAGGAAGAGGAG                         GAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA
genomic: GCATCAGATGAGGAGGAAGAGGAGgtactgctta ... tttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatggttgattgctatgctgtggtttcaatacaatttggatgttttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGATTTGAATCTGATGAGGACTCTCCTCCAAGGAAAACAACCACCCATCGGC
     ggttgat  putative branch site (score: 5)
                                          tgttttctt  putative PPT
                         tttcaatacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttacgagtgtcataagtataggtggaaaataaggatgataccatggttgattgctatgctgtggtttcaatacaatttggatgttttcttgcagGAACCAAAGCAGAAGAACAAGGAGTTTAGAGGCAGTGCCAAAAGGAAGGGATTTGAATCTGATGAGGACTCTCCTCCAAGGAAAACAACCACCCATCGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA