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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttctttgaagatttttggctgttataaataatgtataaaatgctaggttagtcacctgaattatgtacaaaagaatttggtgcagaataaatctta...

Basic information

species Glycine max
transcript GLYMA18G48280.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 11
-TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttctttgaagatttttggctgttataaataatgtataaaatgctaggttagtcacctgaattatgtacaa----aagaatttggtgca-gaataaatctta----------------------------------------------------
 |||||| |||||||||||||||||||| || || ||||| || ||||||||||| || ||||| ||| || ||||||| |||||   ||||||   | | |||   ||   ||   ||  | |     |  ||  ||     |||  | ||   | |    || | | ||   || ||||  | ||||                                                    
ATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAGgtactttcttttctgttcttttattga-gtagcaaagattttcttggtaagagtaactggctgcttcatactccacctcaatattatgacacatgaatgtaacttaatagatcttctatattttttactctacctcaatattttcttgttactttcag

upper sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 10
-TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttctttgaagatttttggctgttataaataatgtataaaatgctaggttagtcacct---gaattatgtacaaaagaatttggtgcagaataaatctta-------------------------------------------------------------------------------------------
 ||| || || ||||||||||| ||||| ||||| |||||||||||||||||||| || || || ||| |  ||||||| ||||||  ||  |      | | |   ||   ||   ||||| || | |   |  |  | || ||   ||||||| || ||   |||||         ||  | ||                                                                                            
ATATCACACACCCAACTCCTGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctatgttttctattcttgagttatcaaatgt-tacactttcacatggggcagctctggaattatttataact-aatttaacattttttattttttttctcatattgatatagaatgtgaagtctttgtttatttttactaccttgatagcttatctgtgttgatgtgatggcattatattctttcag

upper sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G181151_T03 (Zea mays), 5'ss of exon 11
-TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttctttgaagatttttggctgttataaataatgtataaaatgctaggttagtca---cctgaattatgtacaaaagaatttggtgcagaataaatctta-------------------------------------------------------------------------------------------
 ||| || || |||||||| || ||||| ||||| |||||||||||||||||||| || || || ||| |  ||||||| ||||||  ||  ||     ||| |   ||   ||  |||||| || |     |  |  | ||   |  ||||||| || ||   ||||| |       ||  |  |                                                                                            
ATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAGgtgcttttctttgtcttttattcttgagttatctaatgt-tataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcag

upper sequence: GLYMA18G48280.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 5'ss of exon 10
-TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttct---ttgaagatttttggctgttataaataatgtataaaatgctaggttagtcacctgaattatgtacaaaagaatttggtgcagaataaatctta
 |||||| || |||| |||||||||||||||||||||||| || || || || ||| | ||  | |||||  | ||||| |||||  || ||   |    || ||  |  | | |    |  | | |    |  |    | ||    |    ||||||  ||    |||  |  |   |  ||    
ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctcaatccctgaattgggtttatcagtggtgttattttgctttgtgatgttgtgtttttttgtatgtattaatcgcttttttttaatgttgat----

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|192303003|gb|FG997019.1|FG997019
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAG-CAGA                         TATATCCTCCAATCAATGTCCTTCCAT
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCAT
EST: gi|16279334|gb|BI943381.1|BI943381
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGA
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG
EST: gi|16278203|gb|BI942781.1|BI942781
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATNCCTCCAATCA-TGTCCTTCCATCATTG
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATAT-CCTCCAATCAATGTCCTTCCATCATTG
EST: gi|193493069|gb|FK463011.1|FK463011
EST:     TACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGA
genomic: TACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG
EST: gi|193337993|gb|FK302500.1|FK302500
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTG
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTG
EST: gi|16277692|gb|BI942513.1|BI942513
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGA
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG
EST: gi|192296018|gb|FG989412.1|FG989412
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGA
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG
EST: gi|22933182|gb|BU550321.1|BU550321
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGA
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG
EST: gi|16281557|gb|BI944549.1|BI944549
EST:     TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGA                         TATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAAA
genomic: TATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttcttt ... tattgacagaTATATCCTCCAATCAATGTCCTTCCATCATTGTCTCGTTTGATGAAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTACGCATCCAACTCCTGATCTTACAGGATATATTACTGAGGGACAGATATATATCGACAGACAGTTGTATAACAGGCAGGtgggttctttgaagatttttggctgttataaataatgtataaaatgctaggttagtcacctgaattatgtacaaaagaatttggtgcagaataaatctta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaat