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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG

Basic information

species Glycine max
transcript GLYMA16G04690.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g44900.3 (Oryza sativa), 3'ss of exon 3
gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
                            | ||  ||| |       ||| |  ||||   || || | | |  ||||    |||  ||   |  ||   ||| |||| | |  ||| || ||  | ||| |   ||||||||||||||||||| ||| | || ||||| |||||| | |||||||||
-------------------------gagtcttgatttatcaa----ttatcttttttgtcagtttctgtgta-tgttgcaggattttgc--agctcccctttagtctaatgg-tttattttc--aatttgtg-cagGATCCAAAAGAGAAGGCAAAAGCTGAAACAAGAGATTGGCTTAACAATGTG

upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
                                  | ||||| |  ||      |  ||  |  | | || |    |      | |   | | ||  |  ||  | || |   |||||| | ||   | | | |||||| ||||||||||| || || |||||||||||||||||||| |||||||||
---------------------------------atctgttggatattcgtaggtagttatatatatattatatattaacgaaaactcttctctggta--ttcaggct-actgatttgtcagcttcatgttttatagGACCCAAAAGAGAAAGCAAAGTCAGAGACAAGGGATTGGTTGAACAATGTG

upper sequence: GLYMA16G04690.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggt-gttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgact----ttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
                                     |     ||||    | | |   |  || |  ||| ||  |  ||| |   |    || | |  |||           ||| | || | | |    || | |||||| ||||| |||||||||||||||||||||||||| ||||| |||| ||||
-------------------------------------gcaccggttt----aatataaagtactctaatttagtcatgttttaaattttaaaatctaaccttttaatcagattgtttatcatgtaattctttttttgatagGACCCAAAGGAGAAGGCTAAATCAGAGACAAGGGACTGGTTGAACACTGTG

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|209704993|gb|BW667705.1|BW667705
EST:     CTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACT                         GATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
genomic: CTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACTgtgagtcttt ... tttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
EST: gi|213589012|gb|DB973112.1|DB973112
EST:     CTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACT                         GATCCAAAAGAGAAGGCTAAATCAG
genomic: CTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACTgtgagtcttt ... tttctaatagGATCCAAAAGAGAAGGCTAAATCAG
EST: gi|209713189|gb|BW681724.1|BW681724
EST:     CTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACT                         GATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
genomic: CTAAGACCAAAGCATTCTCCAAAGAAGGCTTGGGTCAACAGCCTAAGACTgtgagtcttt ... tttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG
                                      atctgac  putative branch site (score: 3)
                                            ctttct  CT-rich tract
       tttatgtcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctttgaccagggaaatattacctttttgtttgttgtagttttaccactttttggagcttttttttggtgttctttgatcgtgtttatgtcaattttggtctgaggaatttgttatctgactttctaatagGATCCAAAAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTAAACAATGTG

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