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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAATGAATGACAGGGGAGTTTCATATACATTTGGTGCTGATAAGGTCTCAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcctgcctttgtgttcaatgtgttatgccaagtcttcagggttgagtttgtatccccaaatttagttgatgactaaaagtactatgagactta...

Basic information

species Glycine max
transcript GLYMA20G36510.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36510.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G017982_T02 (Zea mays), 5'ss of exon 2
GGGAATGAATGACAGGGGAGTTTCATATACATTTGGTGCTGATAAGGTCTCAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaa---actcctgcctttgtgttcaatgtgttatgcca-agtcttcagggttgagtttgtatccccaaatttagttg-atgactaaaagtact--atgagactta--
                    ||||||  ||||||||| ||||||| || ||||| |||||| | || ||||||||||| ||||| || || || |||||||||       || |     ||||  | |  | |||    | |  || ||  ||  |       |   |  ||    ||| ||   | ||| | ||  ||    ||    
--------------------TTTCATTCACATTTGGTCCTGATAAAGTTTCAGAATTTCTTGAGAAGCATGATTTGGACCTTATCTGCCGAGCACATCAGGTTGTTGTGTTCTTAAAGATgtgacctacttattaccttataaactacaaagtgtatcaatagtttacttatgcttttgcattgttgaaattgcttgattgatctccag

upper sequence: GLYMA20G36510.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0036g00370.t01 (Vitis vinifera), 5'ss of exon 2
GGGAATGAATGACAGGGGAGTTTCATATACATTTGGTGCTGATAAGGTCTCAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgt--taaactcctgcctttgt-gttcaatgtgttatgccaagtcttcagg--gttgagtttgtatccccaaatttagttgatgactaaaagtactatgagactta
|||||||||||||||||||||||| |||||||| ||  |||| || ||  ||||||||||| | || |||||| |||| ||| |||||||||||||||||||   |||||      |  || |||   | | | || || |   |  | |  ||||||||  ||||     || || |  |  |||   || | | |      ||
GGGAATGAATGACAGGGGAGTTTCTTATACATTCGGCCCTGACAAAGTGACAGAGTTTCTTGAGAAGCATGATCTGGACCTTGTTTGTCGTGCTCATCAGgtatcaaacttgattgtcagtagttgtttatttcatacctatattataagcagttgagttcatatc-----atctactctactacttgtaggattgtagagaata

upper sequence: GLYMA20G36510.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S22_185V6.1 (Physcomitrella patens), 5'ss of exon 3
GGGAATGAATGACAGGGGAGTTTCATATACATTTGGTGCTGATAAGGTCTCAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcctgcctttgtgttcaatgtgttatgccaagtcttcagggttgagtttgtatccccaaatttagttgatgactaaaagtactatgagactta--
||||   |||||| | |||||||| || ||||||||| | |||| |||||| |||||||| ||||||||||| ||||||||||| || || || ||||| ||     |     |  | ||    |     | | | || |    || ||  | |   | |   | |||  | |  ||   |  |  || |    | || |  
GGGAGATAATGACCGAGGAGTTTCCTACACATTTGGTCCAGATACGGTCTCTGAGTTTCTCCAAAAACATGACTTGGATCTTATCTGCCGAGCCCATCAAgtactgttatccacactatgaattactcactgttctaatttgaaagcgtctaatc-atgtgttctaatgaaatatattgttgcacttagt-catgcctgaag

upper sequence: GLYMA20G36510.1 (Glycine max), 5'ss of exon 2
lower sequence: EFJ32796 (Selaginella moellendorffii), 5'ss of exon 2
GGGAATGAATGACAGGGGAGTTTCATATACATTTGGTGCTGATAAGGTCTCAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcctgcctttgtgttcaatgtgttatgccaagtcttcagggttgagtttgtatccccaaatttagttgatgactaaaagtactatgagactta
|||   ||||||  | || || |||| ||||||||||    |   |||  | ||||||||||||||||| ||  | ||||| |||||||| |||||||||||   |    |||   || ||||  | | |  ||    |  || ||      || || |    |||    ||                            
GGGTCAGAATGATCGAGGTGTCTCATTTACATTTGGTAGCAACGCGGTTGCGGAGTTTCTTCAAAAACAGGACCTCGATCTCATTTGTCGAGCTCATCAGgtatga----tgctcgtgagttctttctttattgtt--gctttgagccccatgtctgcaataacaataacag----------------------------

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|207829318|gb|GD798168.1|GD798168
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|193637849|gb|FK578581.1|FK578581
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208341446|gb|GE134158.1|GE134158
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208141233|gb|GD938263.1|GD938263
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTA
EST: gi|207751513|gb|GD722526.1|GD722526
EST:     GTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: GTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207758517|gb|GD730243.1|GD730243
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTT
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTT
EST: gi|208080221|gb|GD878089.1|GD878089
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTA
EST: gi|10253235|gb|BE821001.1|BE821001
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208092617|gb|GD888464.1|GD888464
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAAGCTTGTAACAAT
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCA-GCTTGTAACAAT
EST: gi|208134084|gb|GD926991.1|GD926991
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTTATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207844687|gb|GD813990.1|GD813990
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATGG
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGG
EST: gi|208058533|gb|GD860650.1|GD860650
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|207826574|gb|GD798677.1|GD798677
EST:     GTCGTGCTCATCAG                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: GTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208062531|gb|GD860567.1|GD860567
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|15000834|gb|BI321648.1|BI321648
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|41146306|gb|CK606517.1|CK606517
EST:     CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAN                         GTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|208325419|gb|GE123651.1|GE123651
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
EST: gi|9204100|gb|BE330324.1|BE330324
EST:     CAGAGTTTCTTCANAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAAGATTGGGTAT-AGTTCTGTGCTGACCGGCAGCTTGTAACAAT
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGAT-GGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAAT
EST: gi|193646546|gb|FK591745.1|FK591745
EST:     CAGAGTTTCTTCAGAAACATGATTTGGATCTTATTTGTCGTGCTCATCAG                         GTGGTGGAGGATGGGTACGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA
genomic: CAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcc ... ttttgaacagGTGGTGGAAGATGGGTATGAGTTCTTTGCTAACCGGCAGCTTGTAACAATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGAATGAATGACAGGGGAGTTTCATATACATTTGGTGCTGATAAGGTCTCAGAGTTTCTTCAAAAACATGATTTGGATCTTATTTGTCGTGCTCATCAGgttaaactcctgcctttgtgttcaatgtgttatgccaagtcttcagggttgagtttgtatccccaaatttagttgatgactaaaagtactatgagactta

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