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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggttacactttttcatttttcacag

Basic information

species Glycine max
transcript GLYMA18G49770.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaa-tggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggttacactttttcatttttcacag-----------
||| ||||| |||||||| || ||||||||||| ||  | |||||||||||||||||||| || ||||||||||| ||||| || |||||||| |||||||| | ||  | ||||     |||  | |  |  ||    ||   |   |   ||  | | ||||  ||   |||||||| ||                  
ATGCAATGTTAAGATTGCAGACTTTGGCTTGAGTAATGTTATGCGTGATGGTCACTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCAGCACCTGAGgtatttatcttgaatgatttgcattattactccttcttcatgattgcataattgcttctatctttctttacctttttcaattccttttccatttgactag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggttacactttttcat----ttttcacag
||| ||||| |||||||| ||||||||||| || || || ||||||||||||||||||||||| || |||||||| ||||| || |||||||| |||||||| |    | | |||     |||  |   |  || | | | |  || |   | | |   |     | |||| |||   |    |||||  ||
ATGCAATGTTAAGATTGCCGATTTTGGCTTAAGTAATATTATGCGTGATGGTCACTTTCTTAAGACGAGTTGTGGTAGCCCGAATTATGCAGCACCTGAGgtatcatctagcataatttacaattagcgtccttcatggt-tgcatttacatatataacttgccatgacacgtttctgtcttattttcttag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G180704_T01 (Zea mays), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatat-atgtgtgtgtgtgtgtcttggttacacttttt----catttttcacag--------------------
||| ||||| |||||||| ||||||||||| || ||  | ||||| |||||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||  |   |  |  | | | |||  ||   |   |||||   || |  |  || ||   || ||   ||| | |||     ||      ||||                    
ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttctataataggtcaaagata--taaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaac--aattattgttgaggatatatatgtgt-gtgtg-tgtgtcttggttacactttttcatttttcacag
||| ||||| |||||||||||||||||| |||||||||| ||||| |||||||| ||| | || |||||||||||||| || || ||||| ||||| |||||  ||  |  |   | | |  |    |  | |  |     ||    ||| |    || |  ||  | ||     | | | | || |  |||
ATGCAATGTAAAGATTGCTGATTTTGGCCTGAGCAACATAATGCGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGTCCAAATTATGCCGCTCCAGAGgtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgtttcag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgagg-atatatatgtgtgt-gtgtgtgtcttggttacactttttcatttttcacag-----
 |||||| | |||||||| || ||||| ||||| ||  | ||||| |||||||| ||||| || || |||||||||||||| ||||| || ||||| ||||| | || |  | || |       |||| || || |   || |   | ||| | || | | |  ||  |    | | || |  |||         
GTGTAATATTAAGATTGCAGACTTTGGGTTGAGTAATGTTATGCGGGATGGTCATTTTCTAAAGACGAGTTGTGGAAGCCCCAACTACGCTGCTCCCGAGgtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatgagtgtcttatctcttacttcttgttgtag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 5'ss of exon 4
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgt-------ttgtaa---tggaatacacggcaac----aattattgttgaggatata---tatgtgtgtgtgtgtgtcttggttacactttttcatttttcacag--------------------------
||| ||||| ||||||||||||||||| || || || |||||| | |||||||| ||| | || ||||||||||||||||| || ||||| || || |||||       ||| |    |  |||| | | |||     |||| ||| |   || ||    ||      | | |      || | | | |  || |  ||||  ||                          
ATGCAATGTGAAGATTGCTGATTTTGGTTTAAGTAATATCATGAGAGATGGTCATTTTTTGAAGACAAGTTGTGGAAGCCCAAATTATGCTGCCCCAGAGgtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagttacaatactttctaatatatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 5'ss of exon 3
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgta---atggaatacacggcaa------caattattgttgaggatatatatgtgtgtg-tgtgtgtcttg-gttacactttt--tcatttttcacag
||| || |||||||| |||||||| ||  ||  ||| || ||| | |||||||||||||| ||||| ||||| |||||||| || ||||| ||||| |||||||      |||   |   |   ||      |||   |   |||   ||  | ||| | || ||||  |||    ||| |||||   | |  | || |||
ATGGAACGTCAAGATAGCTGATTTCGGACTGTCCAATATTATGAGGGATGGTCACTTTCTCAAAACTAGTTGCGGAAGCCCCAATTATGCTGCTCCAGAGgttttcctccatgccttttcctttaaatatgacaaccttctctgatactac-tttgtatatgatgtgcttctgatattaaactttagataaagtatctcag

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ35371 (Selaginella moellendorffii), 5'ss of exon 3
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggttacactttttcatttttcacag
 || ||||| |||||||| || ||||||||||| || |||||||| ||||| |||||||| ||||| || |||||||| || |||||||| ||||| |||||  |    |   | |          || |  |  || |    | |   | |  |                                 
GTGCAATGTGAAGATTGCGGACTTTGGCTTGAGTAATATCATGCGAGATGGACACTTTCTGAAAACGAGCTGTGGAAGTCCAAACTATGCCGCTCCAGAGgtaagcttcgactttctt--------ttttcctctagaaagccttttcctttcag---------------------------------

upper sequence: GLYMA18G49770.1 (Glycine max), 5'ss of exon 5
lower sequence: EFJ17922 (Selaginella moellendorffii), 5'ss of exon 3
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgt-gtgtgtcttggttacactttttcatttttcacag
||| | ||||||||| || ||||||||| |||||||||| ||||| || ||||||||||| |||||||| |||||||| || |||||||| ||||| |||||         | || |     | || | ||||    |     |   | |  || || | |||   | |||                  
ATGCAGTGTCAAGATCGCGGATTTTGGCCTGAGCAACATTATGCGAGACGGTCACTTTCTGAAAACAAGCTGTGGAAGTCCGAACTATGCTGCTCCAGAGgtc--------agtatatcaggataagttttgtcataggctcgtcattctaagttgtctttctcaatcacag-----------------

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|23731437|gb|BU763843.1|BU763843
EST:     GTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
EST: gi|254315447|gb|GR825256.1|GR825256
EST:     GTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
EST: gi|254336679|gb|GR842858.1|GR842858
EST:     GTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAG                         GTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT
genomic: GTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatg ... tttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTAATGTCAAGATTGCTGATTTTGGCTTGAGCAACATCATGCGTGATGGTCACTTTCTTAAAACAAGTTGTGGAAGCCCTAACTATGCAGCTCCTGAGgtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggttacactttttcatttttcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC