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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtctttgacacagggaaatatgcttttttattttatttttatttttggcttttctaggtgtattatgattatgcttcctttttaggggatgaagagtatcttattctcaatgctttgtgacag

Basic information

species Glycine max
transcript GLYMA16G26850.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26850.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G18230.1 (Arabidopsis thaliana), 5'ss of exon 3
CAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtctttgac-acagggaaatatgcttttttattttatttttatttttggcttttctaggtgtattatgattatgct--tcctttttaggggatgaagagtatcttattctcaatgctttgtgacag
 ||||||||||||   || ||||| || || ||||| ||||| || ||||| ||||||||||| |||||||| |||||  | ||||| || ||||||||||| ||  |||  | ||       |    |  ||||  || |    |   |  |  | |  |  || | | |  || | ||  | |  || |  |  |  |                              
GAAGCTTATTGAGAAAGAGATGGAGAGGTTTAAGATATGTGAAAAAGAGACCAAGACAAAAGCCTTCTCCAAGGAAGGACTGGGTCAGCAACCTAAAACTgtaagaatttctctacttttccgttgaatcatttaccttttccccaaaataagaatgtgaaattgaagtgtttttctactatttcccttcaaagtttcta------------------------------

upper sequence: GLYMA16G26850.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 5'ss of exon 3
CAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtctttgacacagggaaatatgcttttttattttatttttatttttggcttttctaggtgtattatgattatgcttcctttttaggggatgaagagtatcttattctcaatgctttgtgacag
 |||||||| |||||||||||||||||||| ||||| ||||| || || || ||||||||||||||||||||||||||  | || ||||| ||||||||||| ||| || ||||| |       | ||     || ||      |      |  |||||    ||| | |  |||  | |  | ||||   | |   |                             
GAAGCTTATCGAGCGTGAAATGGAAAGATTTAAGATATGTGAAAAAGAAACTAAGACAAAAGCATTCTCCAAAGAAGGGCTGGGCCAACAACCTAAAACTgtaagttttagacactgtcttgctttctgcccaatgttgaaccaagcacatgaatttctgatagtaatttt-ttaatcatggtctttaatagttatggttc--------------------------

upper sequence: GLYMA16G26850.1 (Glycine max), 5'ss of exon 3
lower sequence: PP1S101_120V6.1 (Physcomitrella patens), 5'ss of exon 4
CAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtctttgacacagggaaatatgcttttttattttatttttatttttggcttttctaggtgtattatgattatgc-ttcctttttaggggatgaagagtatcttattctcaatgctttgtgacag
 ||||  || ||| | |||||||||||||| ||  | ||||||||||| || |||||||||||||| |||||||||||| | |||||||| |||||||| ||  |||| | ||    |   | || | ||   ||| |||  ||  | | |  ||    || |  | | || ||  |  || |||  ||  |  | |   | |                         
GAAGCAGATAGAGAGAGAAATGGAAAGATTTAAAGTATGTGAGAAGGAAACCAAGACAAAAGCATTTTCCAAAGAAGGCCTGGGTCAACAACCTAAAACGgtttgtctct-actttcgcgtacatacattccgattgtatgctt--tatcgaattgatcagctagaatttgcttgggaattgcttcatattgacttagtggaa-------------------------

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|208297987|gb|GE095792.1|GE095792
EST:     CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
EST: gi|209718497|gb|BW677667.1|BW677667
EST:     CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
EST: gi|208218115|gb|GE016553.1|GE016553
EST:     AAGACAAAAGCATTCTCCAAAAGAAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: AAGACAAAAGCATTCTCC-AAAG-AAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
EST: gi|207846424|gb|GD819455.1|GD819455
EST:     CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
EST: gi|213615319|gb|DB963513.1|DB963513
EST:     CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
EST: gi|213616529|gb|DB967179.1|DB967179
EST:     CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
EST: gi|208097464|gb|GD896363.1|GD896363
EST:     CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACT                         GATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG
genomic: CAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtcttt ... tttgtgacagGATCCTAGAGAGAAGGCTAAATCAGAGACAAGGGATTGGTTGAACAATGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGCTTATTGAGCGTGAAATGGAAAGATTCAAGATCTGTGAGAAGGAGACAAAGACAAAAGCATTCTCCAAAGAAGGCTTAGGTCAACAGCCTAAAACTgtgagtctttgacacagggaaatatgcttttttattttatttttatttttggcttttctaggtgtattatgattatgcttcctttttaggggatgaagagtatcttattctcaatgctttgtgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG