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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgcttaccgttattgttgcttttatcacgttacacgtgtgaggaattttgtgtgtgaagtttcattttcgttgattgcgtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT

Basic information

species Glycine max
transcript GLYMA13G18660.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g56550.1 (Oryza sativa), 3'ss of exon 1
-gtaacgcttaccgttattgttgctt-ttatcacgtta-cacgtgtgaggaattttgtgtgtgaagtttcattttcgttgattgcgtttgtc------cagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT
 ||| |  |  | || ||||  || | ||||    ||| |   ||| |   ||  ||    || |     || |    |     | | || |      |||| ||||| ||| |  |||||||||| |||||||| || ||||||||||||||||| ||||| || ||  | | |||||| |||||||| ||||| |||||
tgta-cagtgcctgtaattgaggcatgttatgttcttatcttctgtaatctatcatgcacatgcacacctatataatgtaccaacttgtgccaaaccacagGCAAGACCACTCTCTTGAAGATTCTTGCGGGGAAACATATGGTTGGAGGAAGAGATGTTGTCCGTGTTCTTAATGGTTCTGCTTTTCATGACACACAGCT

upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G075336_T02 (Zea mays), 3'ss of exon 1
----------gtaacgcttaccgttattgttgcttttatcacgttacacgtgtgaggaattttgtgtgtgaagtttcattttcgttgattgcgtt--tgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT
          ||| ||||| ||      | ||   ||  ||  ||    | || |   ||||| |||   | |  | ||   | ||  ||  |    |   |||| ||||| ||  |  |||||||||| ||||| ||||| ||||||||||||||||| || || || ||| | | ||||||||||||||| || || |||||
agtgcttcatgtagcgctttccagccgagatgtggtttccagctttgctgagtaa---attttatgtacaacggcttatgcac-ttacttatgccaatactcagGCAAGACCACACTCTTGAAGATTCTTGCGGGAAAGCATATGGTTGGAGGAAGAGATGTGGTCCGTGTCCTCAATGGTTCCGCTTTTCATGATACACAGCT

upper sequence: GLYMA13G18660.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g03680.t01 (Vitis vinifera), 3'ss of exon 1
-gtaacgcttacc--gttattgttgct-----tttatcacgttacacgtgtgaggaattttgtgtgtgaagtttcattt--tcgttgattgcgtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT
  |     || ||  || ||   ||||     | ||  |   | ||  |   ||      |  || | |  || | ||   | |||| | |  | | | |||| || || |||||||||| |||| |||| ||||||||||||||||| || ||||| || ||||  || |||| | |||| |||||||||||||| || ||
gtttgaatttgcctggtgatctgtgctgaggctatacaagaattcaacttcaagacgacgt-cgttttagcttcccttcaattgttgctcgtatct-tgcagGGAAAACCACTTTGCTGAGGATTTTGGCAGGGAAGCACATGGTTGGCGGGAGAGATGTGGTGCAGGTGTTGAATTGTTCGGCTTTTCACGACACCCATCT

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|213618140|gb|DB965297.1|DB965297
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|192305550|gb|FG994316.1|FG994316
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|6341834|gb|AW164658.1|AW164658
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|298190455|gb|HO032576.1|HO032576
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|298196491|gb|HO041234.1|HO041234
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCA                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|151400588|gb|EV270402.1|EV270402
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|192309352|gb|FK000560.1|FK000560
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|151394486|gb|EV264357.1|EV264357
EST:     CAACGTCTCTCTCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
EST: gi|298185222|gb|HO030435.1|HO030435
EST:     CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCG                         GAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA
genomic: CAACGTCTCTCCCGGATCCCGCTGCCTCCTCGTCGGTGCCAATGGATCCGgtaacgctta ... gtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtgtgaggaattttgtgtgtgaagtttcattttcgttgattgcgtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT
                                   cgttgat  putative branch site (score: 5)
                                              tttgtcc  putative PPT
                          tttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgcttaccgttattgttgcttttatcacgttacacgtgtgaggaattttgtgtgtgaagtttcattttcgttgattgcgtttgtccagGAAAGACGACTTTGCTGAAGATTCTGGCGGGGAAGCACATGGTTGGAGGAAGAGACGTTGTGCGCGTCTTGAGTGGTTCCGCTTTTCACGACACTCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT