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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaatttgtttactcctttgaatttcattttttttcttagtgaattgttaagagagatgtcacagtgaatttgtttactcctttgttattgttgttggatttcccctcttttgtttgcaatttctaatttctaattgctatgttgctaacag

Basic information

species Glycine max
transcript GLYMA08G46850.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46850.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g54860.1 (Oryza sativa), 5'ss of exon 3
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaatttgtttactcctttgaatttcattttttttcttagtgaattgttaagagagatgtcacagtgaatttgtttactcctttgttattgttgttggatttcccctcttttgtttgcaatttctaatttctaattgctatgttgctaacag
|||  ||||||| |||   || ||||| ||||| |  || |||||  | ||    |||||||| |||||||||||||| ||||||||||| |||      |      |      |  ||   ||| | ||  | |  ||     ||   ||   |   |     | | | |  ||  |   | || |||  ||                                                                
GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGGgtaagtttccattcctccaagg--agtagctgtgttgtaattgttgtgattggactgt---ttaccagcggtagatttataatagatcgggccattcatttagta----------------------------------------------------------------

upper sequence: GLYMA08G46850.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g54890.2 (Oryza sativa), 5'ss of exon 3
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaatttgtttactcctttgaatttcattttttttcttagtgaattgttaag-agagatgtcacagtgaatttgtttactccttt-gttattgttgttggatttcccctcttttgtttgcaatttctaatttctaattgctatgttgctaacag
|||  ||||||| |||   || ||||| ||||| |  || |||||  | ||    |||||||| |||||||||||||| ||||||||||| |||      || |    |||  ||   | ||     | |  |  || || | | || |||||| |  |||  |       || ||  | | | || ||| ||| ||                                                              
GGTTCTGAGGCTGCAGCCTGGGCACAAGTACTGCCTCCTCGGCCAGCTCTCCAAGGAGGTTGGCTGGAACTACTATGACACCATCAGGgtaagt------ttcc----attccttcctttctagctgtgtggtaattgttgtgattggattgtttaccagatgtagatttatggatcgggtcattcatttagttttta-------------------------------------------------------------

upper sequence: GLYMA08G46850.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G072315_T01 (Zea mays), 5'ss of exon 3
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaatttgtttactcctttgaatttcattttttttcttagtgaattgttaagagagatgtcacagtgaatttgtttactcctttgttattgttgttggatttcccctcttttgtttgcaatttctaatttctaattgctatgttgctaacag
|||  ||||||| ||    |||||||| ||||| |  || ||  |  | ||    ||||| |||||||||||| |||| |||||||||||||||| || |   ||   ||||  ||  || |   | |  |||  |||| |     | |   || |   |  |||  |  |   || | | | |   |  ||| |                                                              
GGTCCTGAGGCTGCAACCTGGACACAAGTACTGCCTCCTTGGTGAGCTTTCTAAGGAGGTCGGATGGAACTACCATGACACCATCAGGgtgagtgttt-cccactcatattttcttgatcat--aagtggcatcgttttgc---acggacactttaatcacttgttgc--tagtttgggtgagttagtaattaata-------------------------------------------------------------

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|213593310|gb|DB975389.1|DB975389
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|209719538|gb|BW669175.1|BW669175
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193553669|gb|FK506260.1|FK506260
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193363286|gb|FK325774.1|FK325774
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAAGGAA
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGA-GGAA
EST: gi|209719537|gb|BW669174.1|BW669174
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGA
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGA
EST: gi|298173139|gb|HO020123.1|HO020123
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAG
EST: gi|58024885|gb|CX711626.1|CX711626
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|151394249|gb|EV264120.1|EV264120
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193701139|gb|FK638652.1|FK638652
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|213615010|gb|DB957048.1|DB957048
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|7041647|gb|AW471599.1|AW471599
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTCGAGAAGAAAATGAATGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193483976|gb|FK449383.1|FK449383
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|15813016|gb|BI785291.1|BI785291
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193728150|gb|FK667650.1|FK667650
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|208338640|gb|GE136064.1|GE136064
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|208205382|gb|GE008313.1|GE008313
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAGAGGAAGGATAGAGCACAATTGTGTTACGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|5057451|gb|AI735927.1|AI735927
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|41146366|gb|CK606577.1|CK606577
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193725749|gb|FK660127.1|FK660127
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|13790079|gb|BG652670.1|BG652670
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATG
EST: gi|7042684|gb|AW472578.1|AW472578
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAA
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|193547600|gb|FK501537.1|FK501537
EST:     GAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: GAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|208304697|gb|GE103546.1|GE103546
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|9899592|gb|BE608560.1|BE608560
EST:     TTGGCCAATTGTCATCTGAGGTTGGATGGATCTACTATGATACCATCAGG                         GAACTCGAGAAGATAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGATG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|208193804|gb|GD990727.1|GD990727
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
EST: gi|192311953|gb|FK004556.1|FK004556
EST:     TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGG                         GAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG
genomic: TGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgctt ... ttgctaacagGAACTTGAGAAGAAAAGGAAGGAGAGAGCACAATTGTGTTATGAGAGGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGTTGAGGCTTCAGAAGGGACACAAATACTGTCATCTGGGCCAATTGTCATCTGAGGTTGGATGGAACTACTATGATACCATCAGGgtgagtgcttgctttctggaatttgtttactcctttgaatttcattttttttcttagtgaattgttaagagagatgtcacagtgaatttgtttactcctttgttattgttgttggatttcccctcttttgtttgcaatttctaatttctaattgctatgttgctaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA