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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacag

Basic information

species Glycine max
transcript GLYMA13G28720.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt------tttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacag
 || ||| | |||||||| ||||| || ||| |||||||||| || |||||||| || || ||||||||||| |||||||||||||||||  | || ||||||   |         || |||  |  | |  |    |    |  | |  |  | | || |  |||     |  ||||||
GAAAAAGCTAGACCGCTATAAGAACCCTTGGTTAGAGTTGAAAATTCAGTATGGCCAGAATAAAGGGAAGTTATACAACGAAGAATGTGATCGTTTTATGgtatgctacaccacaattgttcctgaacaatttaagcccctttcttttttgcattttaacagcttgtgtcta--ttacag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctc------catcatccttctatgggtttctaaaaaaattgctataaatttacag
 |||||||| |||||||| |||||||| ||| |||||||||| || |||||||| || |||||||||||||| || || || ||||| ||| | || ||||||   | | |  | | |  ||    ||      |||     ||| |  |     |    || | | | | |  || |||
GAAGAAGTTAGACCGCTATAAGAATCCATGGTTAGAGTTGAAAATCCAGTATGGACAGAACAAAGGGAAGTTCTATAATGAGGAATGCGACCGTTTTATGgtatgctctatcataccatctcactttctgcacacatttgttttcaaacgtgacatgtctaattagttgtcacatttcag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: GRMZM2G010085_T02 (Zea mays), 5'ss of exon 14
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgcta---taaatttacag-----
 |||||| | |||||||||||||| || ||| |||||||||| || ||||| || ||||| ||||||||||| || ||||| ||||||||| | || ||||||   ||||| |  | | ||   |     | ||   | |  | ||   | | |    | |||   |  | |||||      
GAAGAAGCTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAGTACGGCCAAAATAAAGGGAAGTTCTATAACGAGGAATGTGACCGCTTTATGgtatg-tttttctcaccatgttatgtgtatttatgtattt--gagtacatgacatggctactaagctggagttacattccag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: AC235535.1_FGT001 (Zea mays), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatccttctatgggtt---tctaaaaaaattgctataaatttacag-------------------------
 |||||||| |||||||||||||| || ||| |||||||||| || || ||||| ||||| ||||||||||| || || || ||||||||| | || ||||||    ||   |  | |  |   | |     ||     ||   |||   ||||  ||  | | | | |  || |||                         
GAAGAAGTTAGACCGCTACAAGAACCCATGGTTAGAGTTGAAAATTCAATATGGCCAAAATAAAGGGAAGTTCTATAATGAGGAATGTGACCGCTTTATGgtatg--ttccctcaccatattatgtttatctatgtgagtacatgttatgtctactaagctgggtgtcacattccagctttgcatggtgcacaaacttggat

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaa--tttttttttctaggtct-------agctccatcatccttctatgggtttctaaaaaaattg---ctataaatttacag-------
 |||||  |||| |||||||  || |||||||| ||  ||||||| || ||||| || |||||||||||| ||||||| ||||| || ||| | |||||||||  |  | | ||| || |  |||          | |||  |  || | |   | |   |  | ||||   | || || ||           
GAAGAAACTGGATCGCTACAGAAACCCGTGGCTGGAACTGAAGATTCAATATGGTCAGAACAAAGGGAAGCTGTACAATGAAGAGTGCGACCGTTTCATGgtatgacatctatttatcaaactctttgttgagatttcattgttattgttttattctaatatgatattgacccgatgaacttgtgattatcag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatc-atccttctatgggtttctaaaaaaattgctataaatttacag------------------------------
 ||||||||||| |||||||||||||| ||||| ||  | ||||| |||||||||||||||||||||||||||||||| |||||||| ||  | || |||||   | ||    |  |   ||||| |   |  || |   | | ||| | |       |  | ||  || | | |                              
GAAGAAGTTGGATCGCTACAAGAATCCATGGCTGGAACTAAAGATCCAGTATGGGCAAAACAAAGGGAAGTTGTACAATGAAGAATGCGATCGTTTTATGgtgagaattgcaatcatctctctagtttgtttgatacaaatgttggtgtgtttttgtttgacgattgatcttccgagtgtattcatgcctccatacttcatgtag

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: EFJ32950 (Selaginella moellendorffii), 5'ss of exon 20
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatcc-ttctatgg-gtttctaaaaaaattgctataaatttacag
 |||||  | |||   |||  |||||| |||| |||| |||| || ||||| || ||||||||||| ||| |||||||||| || |||||  | || |||||||   ||        |||| ||    |  || |  ||  |||  |  | |   |                    
GAAGAAACTAGACAAATACCGGAATCCCTGGCAAGAGCTGAAAATCCAGTACGGCCAAAACAAAGGCAAGCTGTACAACGAGGAGTGTGATCGTTTTATGgtacg--ttaagcacgaaggtatactatcgccaccgatttcatgatgcattttgcag-------------------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: EFJ31365 (Selaginella moellendorffii), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacag
 |||||| ||||||| ||||| |||||||||| |||| |||| || ||||| || || ||||| || ||  | ||||| |||||||||||||| ||  |||||   || |||| | |   ||   |  ||        | || | |||||  |                     
GAAGAAGCTGGACCGATACAAAAATCCGTGGCAAGAGCTGAAAATCCAGTACGGTCAGAACAAGGGTAAACTATACAATGAAGAATGTGACAGGTTTTTGgtaagcttgttttgttt--ttcataccacaaaccgtaccgatcgttttctccag--------------------

upper sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 22
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 22
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacag
 |||||| ||||||| ||||| |||||||||| |||| |||| || ||||| || || ||||| || ||  | ||||| |||||||||||||| ||  |||||   || |||  | | | |    |  ||        | || | |||||  |                     
GAAGAAGCTGGACCGATACAAAAATCCGTGGCAAGAGCTGAAAATCCAGTACGGTCAGAACAAGGGTAAACTATACAATGAAGAATGTGACAGGTTTTTGgtaagcttgtttggttttgat---accacaaaccgtaccgatcgttttctccag--------------------

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|24136997|gb|BU927507.1|BU927507
EST:     ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATG                         ATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
genomic: ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt ... aaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
EST: gi|298166870|gb|HO010309.1|HO010309
EST:     ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATG                         ATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
genomic: ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt ... aaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
EST: gi|37997763|gb|CF809352.1|CF809352
EST:     ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATG                         ATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA
genomic: ATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttt ... aaatttacagATATGCATGGTGCACAAACTTGGCTATGGGAACTGGGATGAGTTAAAGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAAGTTGGACCGCTACAAGAATCCGTGGCTAGAGTTGAAGATACAGTATGGGCAAAACAAAGGGAAGTTGTACAACGAAGAATGTGACAGATTCATGgtacaatttttttttctaggtctagctccatcatccttctatgggtttctaaaaaaattgctataaatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA