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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc...

Basic information

species Glycine max
transcript GLYMA01G43470.5
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaag--ttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc-
 |  || ||||| || ||  || | ||||| || ||||| |||||||| || || ||||| |||||||||||| |||||||| |||| ||||| || ||||||  |    |   ||| | |||    |||| || |    |  | || ||  ||  ||||  |  ||||  ||  |     |     ||  ||||    |   
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttc-ctgcaatttaaggtacttggattatcatccgtctaaatctgga--actctgtccgacaatctgccatttttttttag

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcact--tcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
 |  || ||||| || ||| |    || || |||||||| || ||||||||||| || || |||||||||||| |||||||| |||| ||| |||||||||||        ||  |||     | |   ||   ||    |  | |   |   | |  |||   ||  ||    ||      |    ||             
CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatgg--cagcagtttcagataactcgcttgggctaacgacgtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag----------

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
|||||  ||||| || ||  || |  | || ||||||||||| |||||| | |||||||| ||||| ||||||||||| || ||||| |||||||||||||||     | | |||   | | |     |||   ||| |||    |||   | ||| || || |      |  ||   | |||  ||||||||  |    
AAAAGATGTTCATCTGGAACCAGTGGCGTTCGACATGGAACGAGACCTTCTTACTCCAACCTACAAAAAGAAGAGGCCTCAATTGCTCAAATACTATCAGgtaa----ttttaaacattttaggcgatattatgctt-ata----atattttcggttttaaact------ctctttctattgg--tgttatttaacag--

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
 || ||  |||| |||||| || | ||||||||||||||||| || ||| | || || || | ||| ||||| ||||| |||||||| |||||||| ||||||  |     ||||  || |    ||| | |     ||| | |||    |  |   || ||||   |||     ||         || || | ||    
CAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTCAGTTGCTGAAATACTACCAGgtaata-----caaacacttt----tgcgtattgaaacatttagaaatctactgacatt-aagtat-taattaacatggtctcttcgtcatctgccag--

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgta------caagttgtcaaattc-tctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
 |||||||||||||||||| |  | |||||||| |||||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||| |||||||||      |   |  ||| |||| |      ||     |   | | | |  || |||||  | |        | ||   | ||  ||| ||  |  | |       
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataa-tttaagcaaaaagaattatcattgatgaaacctggtctt------

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|208067869|gb|GD866181.1|GD866181
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|193669681|gb|FK607759.1|FK607759
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCCTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|208317694|gb|GE116265.1|GE116265
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|193424751|gb|FK392042.1|FK392042
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG