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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctataaattccaaaagatcttatttacgttacttggttactgacggtcatgttgtgataagaatgaactaacaatagctgttctttttatcttggtaacag

Basic information

species Glycine max
transcript GLYMA05G28260.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G28260.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 9
-TACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtatt-cctataaattccaaaagat-cttatttacgttacttggttactgacgg---tcatgttgtgataagaatgaactaacaatagctgttctttttatcttggtaacag
  | ||  |||||||||||| | ||||||   || || ||||| |||||||| || || ||| | ||||||||||  |||||||||||| | ||||| |||||||  | |     ||       |  ||| || |  | |||    |   | |     |    ||||  | | |||    ||   |  | || ||| | ||| ||  |  |||
CAATACC-GAGAAGATTGAGACTGCTGGGGCAAAGAAAGAAGAGGGGAATGCATTGTTCAAGCTGGGCAAATATGTCAGGGCTTCAAAGCGTTATGAGAAGgtatggcatgcttcttttgttgaacacttgttcaaataactaatctttcgtcaagattttctttgttttcataatcccttactgactgatgatctatctattttattc-cag

upper sequence: GLYMA05G28260.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G336858_T01 (Zea mays), 5'ss of exon 6
TACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctataaattccaaaagatcttatttacgttacttggttactgacggtcatgttgtgataagaatga-actaacaatagctgttctttttatcttggtaacag
       ||||||||||| |||||||  ||||| || |||||||||||||  |  |||||  ||||||| ||||  |||||||| |||||||||||||||||        ||| |  | |  |      |||    || |  |         |    || || ||| || |  | | |  || | | | || ||| ||          
CGTTGCTGAGAAGATTGAAGCAGCTGCTAAGAAGAAAGAAGAAGGGAATGTGTGGTTTAAAATTGGCAAGTATGCCAGGGCTTCTAAGAGATATGAAAAGgt-------caaaatttagagcactgggcttaaagaaccttttgcaccttctttgcattatgctaaaaaaggtatttaagattgttttgctctttctcag--------

upper sequence: GLYMA05G28260.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G096585_T01 (Zea mays), 5'ss of exon 9
-----------------------TACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctataaattccaaaagatcttatttacgttacttggttactgacggtcatgttgtgataagaatgaactaacaatagctgttctttttatcttggtaacag
                        |   |||||||||||||||| ||||| ||||| || || ||||||||||| || || ||    ||||||||||  || ||||| ||| ||||||| |||||  ||                                                                                                     
GACAAGGAGTCGTGGGACTTGAACAATGAAgagaagattgaggctgctggtaagaagaaagaggaagggaatgcattgttcaaatcgggcaaatatgctagagcttccaagcgatatgagaaggtggtct----------------------------------------------------------------------------------------------------

upper sequence: GLYMA05G28260.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 9
TACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctataaattccaaaagatcttatttacgttacttggttactgacggtcatg-ttgtgataagaatgaactaacaatagctgttctttttatcttggtaacag
 |   |||||||||||||||| ||||| ||||| || || ||||||||||| || || ||    ||||||||||  || ||||| ||| ||||||| |||||  || |      |        | |  |  ||  |||  ||  | ||    |  || ||     | |  ||  |  |     ||||    |||| | ||  |  |||
CAATGAAGAGAAGATTGAGGCTGCTGGTAAGAAGAAAGAGGAAGGGAATGCATTGTTCAAATCGGGCAAATATGCTAGAGCTTCCAAGCGATATGAGAAGgtggtcttcc----tttctgttctgtagtaaaccataccgggaaaatgcaatttttgattcctgcagggttgttcctatttgggctgaa--ttttgttttaattgcag

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|19270890|gb|BM887146.1|BM887146
EST:     CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|57574566|gb|CX547541.1|CX547541
EST:     CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|9987554|gb|BE661662.1|BE661662
EST:     CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGANGAGAAACCG
genomic: CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|58023136|gb|CX709877.1|CX709877
EST:     CCTTTTTTAAGGTGGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|58022830|gb|CX709571.1|CX709571
EST:     CAAATATGAAAGGGCTTCAAAGAGGTATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: CAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|58019828|gb|CX706570.1|CX706570
EST:     CCTTTTTNAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|6455054|gb|AW185737.1|AW185737
EST:     AAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: AAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
EST: gi|51334753|gb|CO978619.1|CO978619
EST:     CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAG                         GCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG
genomic: CCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctat ... ttggtaacagGCCATAAAGTTTGTCGAGTATGATTCCTCCTTTAGTGATGAGGAGAAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACACAAGAGAAGATTGAGGCAGCTGGGAAGAAAAAGGAAGAAGGGAATGCCTTTTTTAAGGTTGGCAAATATGAAAGGGCTTCAAAGAGATATGAAAAGgtattcctataaattccaaaagatcttatttacgttacttggttactgacggtcatgttgtgataagaatgaactaacaatagctgttctttttatcttggtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA