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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccattttgacctactttcttttcaactattccctcatgacaaattatattttcttgcaggtttttcatttcattataataatatattaatagtta...

Basic information

species Glycine max
transcript GLYMA05G05860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 5'ss of exon 3
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccattttgacctactttcttttcaactattccctcatgacaaat-tatattttcttgcaggtttttcattt-cattataataatatattaatagtta------
|||||||||||| |||||| |||| || ||| | ||||||||||| || || ||||| || ||||||||||| || | ||||||||||||||||   | |          |||           |     || ||  | | |  |  ||  | | ||||  | |  ||  |    |  | |  || ||  |      
GGATACAGCTGGTCAGGAACGATTCAGGAGTTTGATTCCAAGCTATATCAGAGACTCTTCCGTTGCTGTCATCGTATTTGATGTTGCAAgtatgttctctca--------tctccatgtgcgcacatgggtggcatgtgtgttctcactaactgcttttatactagcaacaatgcagcagaccaacagagaattgcc

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G169694_T01 (Zea mays), 5'ss of exon 3
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgta---tgccattttg----acctactttcttttcaactattccct----------catgacaaattatattttcttgcaggtttttcatttcattataataatatattaatagt-ta-------------------------------------------
|||||| ||||| ||||||||||| || ||| | ||||||||||| ||||| ||||| || |||||||||||||| |  |||||||||||||   | ||  | |     ||  || |||| |  || || |   |          ||| |  ||  | | |  || | |  || |   ||| |      |||    ||||     ||                                           
GGATACTGCTGGTCAGGAAAGATTCAGGAGTTTAATTCCAAGCTATATTAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttttaaaggtttaagcctttaaggacataaacttttactattttgttcttacctttttgtttcatgttgtag

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G075719_T02 (Zea mays), 5'ss of exon 3
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccattttgacctactttcttttca-----actattccctcatgacaaattatattttc--ttgcaggtttttcatttca-ttataataatatattaatagtta------------------------------------------------------------
|||||||||||| |||||||| || || ||| | ||||||||||| || || ||||| || |||||||||||||| |  |||||||||||||  |  | |    ||   |      ||     ||   | | | | || |||  ||  | ||   ||||  |   |     || | |  |  |  | |||    |||                                                            
GGATACAGCTGGTCAGGAAAGGTTCAGGAGTTTAATTCCAAGCTATATCAGAGACTCTTCAGTTGCTGTCATTGTATTCGATGTTGCAAgtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttttatcttttaaggattaaggacataaatttttactattttattcttacctttatttgtttcatgttgtag

upper sequence: GLYMA05G05860.1 (Glycine max), 5'ss of exon 3
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 5'ss of exon 3
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgc-cattttgacctactttctt-----ttcaactattccctcatgac--aaat--------tatattttcttgcaggtttttcatttcat----tataataatatattaatagtta-----------------------------------------------------
|||||||||||| || ||  |||| || ||||| ||||| ||||| || ||||| || || |||||||| ||||| ||||||||||||||||||   |  || ||    | |||          | ||||  | |||  |  | ||        | |  |||   | |   || | | || ||    |   ||    | || ||  | |                                                     
GGATACAGCTGGGCAAGAGCGATTCAGGAGTCTAATTCCGAGCTATATCAGGGATTCCTCCGTTGCTGTTATTGTGTATGATGTTGCAAgtatgtgtaccttcactcgttctctcaaacacatgaatattttcccatatctgagatcttggggatgtggttttcagtaatcttatgaatttatgcgtttcgatttcttctttatgttgatccattgtgcgttgtgaaactcgagatttattttgttttccactgacatatag

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|7146015|gb|AW507937.1|AW507937
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTGTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|21995147|gb|BQ786675.1|BQ786675
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACT
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACT
EST: gi|8284612|gb|BE022171.1|BE022171
EST:     AAGCTACATTAAGGACTCATCTGTAGCTGTCATTGTTTATGATGTTGCAA                         GCCGGAAGACTATCCTAAACACATC
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATC
EST: gi|192325163|gb|FK017534.1|FK017534
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|298193040|gb|HO033474.1|HO033474
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|13252783|gb|BG363686.1|BG363686
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|192321239|gb|FK014329.1|FK014329
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|31459979|gb|CD402007.1|CD402007
EST:     CTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: CTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|192322379|gb|FK014620.1|FK014620
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
EST: gi|192321240|gb|FK014330.1|FK014330
EST:     AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAA                         GCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG
genomic: AAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccatt ... tacgatatagGCCGTCAGACTTTCCTAAACACATCAAAGTGGATTGAAGAGGTGCGCAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACAGCTGGACAGGAAAGATTTAGAAGTCTTATTCCAAGCTACATTAGGGACTCATCTGTTGCTGTCATTGTTTATGATGTTGCAAgtatgccattttgacctactttcttttcaactattccctcatgacaaattatattttcttgcaggtttttcatttcattataataatatattaatagtta

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