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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCTCAGAATAGCTTGTACGTTGGCACAAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttattgcaaaagtattatctcctgatttgtttatttatcagttaagatcaactatattttgaattaatactttactgtctcttttgaataggatg...

Basic information

species Glycine max
transcript GLYMA12G37130.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g10200.1 (Oryza sativa), 5'ss of exon 5
GGAGCTCAGAATAGCTTGTACGTTGGCACAAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatg-ttattgca------aaagtattatctcctgatttgtttatttatcagttaagatcaactatattttgaattaatactttactgtctcttttgaataggatg
||| || ||||||||||||||  | || |||||||||||||| || || |||||||||||| | |||||||| ||||| | | | ||  ||         |||| | | | |   |     ||||||     ||   | || || | | | | || | |   | |    | | ||           
GGAACTAAGAATAGCTTGTACAATTGCTCAAATGGAGCGTGAGGGTGGCATCAGTCCCCGAATGTCACCTTTAGCACAAgtaagattcctgtgcgatctgaagtttgaccccaacaggatattattttgtgcttcgta-cacctttttatggcatcagtttctcagaagcacattcctgg------

upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 7
lower sequence: AT1G22800.1 (Arabidopsis thaliana), 5'ss of exon 7
GGAGCTCAGAATAGCTTGTACGTTGGCACAAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttattgcaaaagtattatctcctgatttgtttatttatcagt--taagatcaactatattttgaattaatactttactgtctcttttgaataggatg
|||||| |||||||| || || ||||| || |||||||| ||||||||||| ||||| ||  ||||||||||||||||||  |||         | |||  |  |  |||    ||  ||   |||  | || | ||           |  |   |||  || |   |||| |        
GGAGCTGAGAATAGCATGCACTTTGGCTCACATGGAGCGGGAAGGAGGGATTAGTCCTCGGCTATCACCTTTGGCACAGgtgtgt------gtgaatatcttagcaagatcaagttgatttctagtactgaggtgaa---------agaacatggcttctcttttctttttcag-------

upper sequence: GLYMA12G37130.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv18s0001g06830.t01 (Vitis vinifera), 5'ss of exon 7
GGAGCTCAGAATAGCTTGTACGTTGGCACAAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgt----tattgcaaaagtattatctcctgatttgtttatttatcagtt--aagatcaactatattttgaattaatactttactgtctcttttgaataggatg
|||||| |||||||| |||||  | |||||||||||||||||||| || || ||||| ||||||||||| ||||||||||   ||    |  ||||||| |  | |||  |   |  || | || | | ||  ||| |||   || | |  | ||   |       || |||| || ||      
GGAGCTGAGAATAGCATGTACTGTAGCACAAATGGAGCGTGAAGGGGGCATAAGTCCACGAGTATCACCATTGGCACAGgtgggtactttgctgcaaaattcctctctatta--tcattaaattgtgacttgaaaggtcagtcat-tatatagttttcaagcagtagtttcttatgcatgca---

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|213593987|gb|DB981371.1|DB981371
EST:     GAGTATCACCTTTGGCACAG                         G-AAGTAGATGCTGGGAATCTTTTGACTAGGGCACAATTCACCCTTCCAGG
genomic: GAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCG-AGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGG
EST: gi|193409851|gb|FK372063.1|FK372063
EST:     AATGGAGCGTGAAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTT
genomic: AATGGAGCGTGAA-GGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTT
EST: gi|6846254|gb|AW348544.1|AW348544
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGG
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
EST: gi|14012032|gb|BG726963.1|BG726963
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCNAGATGCTG
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTG
EST: gi|254345258|gb|GR855808.1|GR855808
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGG
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
EST: gi|192297062|gb|FG990333.1|FG990333
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGG
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
EST: gi|15200173|gb|BI424211.1|BI424211
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
EST: gi|6071750|gb|AW101137.1|AW101137
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGG
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
EST: gi|51335049|gb|CO978915.1|CO978915
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGG
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
EST: gi|192299412|gb|FG992530.1|FG992530
EST:     AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAG                         GTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT
genomic: AAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttatt ... ccattttcagGTTCGAGATGCTGGGAATCTTTTGACTAGGGCAGGTTTCACCCTTCCAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCTCAGAATAGCTTGTACGTTGGCACAAATGGAGCGTGAAGGAGGGATCAGTCCCCGAGTATCACCTTTGGCACAGgcatgttattgcaaaagtattatctcctgatttgtttatttatcagttaagatcaactatattttgaattaatactttactgtctcttttgaataggatg

- - - - - - - - - - - - - - - - - - - -  AAGGAG