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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagttctagtgataggtttgtcatttgtgcaccttggtgtcattaaaatggattatactaacttgcatattaaacattttattttttaaaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC

Basic information

species Glycine max
transcript GLYMA20G23310.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 1
gtagttctagtgataggtttgtcatttgtgcaccttggtgtcattaaaatggattatactaac----ttgcatattaa-acattttatttttta--aaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
         | || |   ||| | ||||    || |  ||   || |  |   ||||    |     | || | | |   |   | |||||      |     |||||| || |||||||| |||||||||||||| |||||||| || || || || ||||| || || || || || ||||| || |||||||| || ||||| |
-------gggggaaaccgttgccttttgctttccgtactgaacttgagttttgttatgtatatggggtcgcgtgtaaccgcggctgattttccgctgatccttccagGTGAAGGAGATCCTCATCGAGGAGTCCAACGTGCAGCCAGTGAACAGCCCGGTGACCGTGTGCGGAGACATCCATGGGCAGTTCCATGACCTGATGAAGC

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 1
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 1
gtagttctagtgataggtttgtcatttgtgcacct-tggtgtcattaaaatggattatactaacttgcatattaaacattttattttttaaa-ataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
  |||  |     | |   |  ||   ||   | | |  | |||| | ||||  ||      |    |   | |  ||    || |||| |  ||     |||| ||||| || ||||| ||||| || ||||| || |||||||| ||||| || || || ||||||||||| ||||| || || |||||||| |||||||
--agtgttgaaacttgtagtagcagccgtcttcttcttttttcatgacaatgatttgctaagatactctggtaattcacaagatattttgactattatatagGTGAAAGAAATTCTTATTGAGGAATCAAATGTACAACCTGTCAACAGTCCTGTCACCGTCTGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAAC

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 1
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 1
----gtagttctagtgataggtttgtcatttgtgcacct-tggtgtcattaaaatggattatactaacttgcatattaaacattttattttttaaaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
        || ||  |     ||| |||    |  |  | | |  |    || ||| || ||  |     |   |  | |   | | | |  |||  |    ||||| |||||||| || || |||||||| || || |||||||| || |||||||| || || ||||||||||| ||||| || || |||||||| ||||| |
agataccattttatggtctcctttctcagcgattgatttatagatttgcgaagatgaatcatggt-----gttaaccagaagatgtttatcataatgttatacagGTGAAAGAGATTCTGATTGAGGAGTCAAACGTACAGCCTGTAAACAGTCCAGTCACCGTATGTGGTGATATCCATGGCCAGTTTCATGATCTTATGAAGC

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 1
gtagttctagtgataggtttgtcatttgtgcaccttgg-tgtcattaaa-atggattatactaacttgcatattaaacattttattttttaaaatacc----ccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
    ||||||  | |       |||||| |    ||      || | || | |  |||||    | | |||  | | |   | | |  |  |  | |       |||||||||||||||| || || ||||| ||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||||||||||||||||
----ttctaggcaaaaaac--acatttgggtgttttaaacaacactgaataagttttatagctgcctccatgcttatctgatgactgatatatgttctatatttagGTAAAAGAGATCCTCATTGAAGAGTCTAATGTTCAGCCTGTCAATAGTCCAGTCACTGTTTGTGGTGATATTCATGGCCAGTTCCATGATCTAATGAAAC

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 1
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 1
---gtagttctagtgataggtttgtcatt-tgtgcacct---tggtgtcattaaaatggattatactaacttgcatattaaacattttattttttaaaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
      |||  ||  ||  ||   || || ||   |      |||| ||  |   || | |  |  | |||| |||   |||| || | || ||      | | ||||| ||||| ||  |  | ||||| |||||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || || |||||  | ||||| |
ctctgcgtttgagaaattagtccttctttatggttatacgaatggtctcgctggcatcggtgttcatgactttcat--caaactttgttttgttc-----atcgcagGTGAAAGAAATATTGGTGGAGGAATCCAATGTTCAGCCTGTCAACAGTCCCGTTACTGTTTGTGGCGATATCCATGGCCAGTTTCATGACTTGATGAAGC

upper sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 1
gtagttctagtgataggtttgtc-atttgtgcaccttggtgtcatta-aaatggattat-----actaacttgcat-attaaacattttattttttaaaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
       |   |  || | | |    ||||||     | | |||    | ||||  | |     | |   || |||   | || |   | | ||||    | || ||||| ||||| ||  | || |||||||||||||| ||||||||||| ||||| || ||||||||||| ||||||||||| ||||| |||||  ||||||| |
-------tgccgtcagctctatttggttgtgcgaggggttatcagcgcagatggcctctctggcattgtttttcattgctcaataaactctcttttgtc-tcccgcagGTGAAAGAAATATTGATGGAGGAGTCCAATGTTCAGCCTGTCAACAGTCCTGTTACTGTTTGTGGCGATATTCATGGACAATTTCATGACTTAATGAAGC

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|213610750|gb|DB963136.1|DB963136
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|213588325|gb|DB967811.1|DB967811
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATTGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|254318584|gb|GR832752.1|GR832752
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|298191713|gb|HO035795.1|HO035795
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCGGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|37994239|gb|CF805985.1|CF805985
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGCCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|18719747|gb|BM523222.1|BM523222
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|192305488|gb|FG998300.1|FG998300
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
EST: gi|6567303|gb|AW234914.1|AW234914
EST:     AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATAT                         GTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA
genomic: AAGAGGGCCAGCATCTTCTTGAAGACGAGCTTCAACTTCTCTGCGAATATgtaccccttc ... aataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatggattatactaacttgcatattaaacattttattttttaaaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC
           tactaac  putative branch site (score: 0)
       attatactaacttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttctagtgataggtttgtcatttgtgcaccttggtgtcattaaaatggattatactaacttgcatattaaacattttattttttaaaataccccagGTAAAAGAGATCCTTATCGAGGAGTCCAATGTGCAGCCTGTCAATAGTCCAGTGACTGTTTGTGGTGATATTCATGGTCAATTCCATGATCTAATGAAAC

- - - - - - - - - - - - - - tgcacct
- - - - - - - - - - - - - - - - - -tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat