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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttag

Basic information

species Glycine max
transcript GLYMA15G20400.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G20400.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 5'ss of exon 4
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaact-gatatattttcattccttttattttag
|  ||||| ||| | || || || ||  | |||||||| || ||||||   ||  | ||||||||||| ||||||||||| ||||||||||| ||||| |||  |   ||| |||  | |||  |  ||  | || ||| |   ||      ||||        |  | |||||  ||  |||   | | |   | || |  ||  ||               
AGCATTCTTGGACTGGAACCAGGTGCATCAGAGTCTGATATCAAGAAATCATACCGTAGACTTTCTATCCAATACCATCCTGATAAAAATCCTGATCCTGgtaaagtttgtctcacatttttgataatc--aatggtgctaaataaga---aatgt--------agctgggcttattattattatttttttgttttgaaactttcccag--------------

upper sequence: GLYMA15G20400.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G007871_T02 (Zea mays), 5'ss of exon 3
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttag
| |||||| ||| | ||  |||| ||  |||| ||||| || ||||||   |||||||||||||||||||| |||||||| ||||||||||| |||||||||          ||| ||||  |    | | ||   |    |   ||| ||| |   || || ||        || |||  | |   |     || |    |||||   |          ||
AGTATTCTTGGACTGGAAGCTGGGGCATCTGAATCTGATATCAAGAAATCATATAGGAGACTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgt-------acctcatttgt--aacactataataaat----tattaatgttgctcaatgaagaaaaaata-tatcttacc-tggtgaactcttcttacgccttttctcccacacatacccag

upper sequence: GLYMA15G20400.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G167868_T01 (Zea mays), 5'ss of exon 3
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttag
| |||||| ||| | ||  |||| ||  |||| ||||| || ||||||   |||||||| ||||||||||| |||||||| ||||||||||| |||||||||      | ||  |    | || |  |  | ||    ||||| | |     || | | |     ||  |    | ||  |||  || |    |  | | |                     
AGTATTCTTGGACTGGAATCTGGGGCATCTGAATCTGATATCAAGAAATCATATAGGAGGCTTTCTATTCAGTACCATCCTGATAAAAATCCTGATCCAGgt-acctcttttgtaacattataataattctgtt----caatgaagaaaaaaatatat-cttacctggtgaacacttatgatt-tctctcccgcctacacag--------------------

upper sequence: GLYMA15G20400.1 (Glycine max), 5'ss of exon 4
lower sequence: AT4G21180.1 (Arabidopsis thaliana), 5'ss of exon 4
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaag-gtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttag
  ||| || || || || ||||| ||  | || || ||||| ||||||   ||||| ||||| ||||||||||||||||| ||||||||||| ||||||||| |||  |  |    ||  | |   ||  | || |||  | | |     ||    |     |  ||||    ||| ||  ||||| ||| |   |  | || |   |               
GGTATACTCGGTTTGGAACCTGGTGCTTCAGATTCAGAAATCAAGAAAGCATATAGAAGACTCTCTATTCAATACCATCCTGATAAAAATCCTGATCCAGgtcgaaatgcttcctggtcctcttccttgataatcgtt-tatttcctcccttttgatacattgttatgtg---ttcttagtattgcttatttgtgtattgtaatggtacag------------

upper sequence: GLYMA15G20400.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G79940.3 (Arabidopsis thaliana), 5'ss of exon 4
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttag
| ||| || ||| | || |||||||   | || || ||||||||||||   ||||| || || || |||||||||||||| ||||||||||| |||||||||  ||| | || |  |||||   |||| ||    ||   || ||       ||  | |  | |   |  | | |  | | ||   | |   |     || | || ||  ||          
AGTATACTTGGACTGGAACCTGGAGTTACAGATTCAGAAATAAAGAAAGCATATAGAAGGCTGTCGATTCAATACCATCCTGATAAAAATCCAGATCCAGgtc-aagtttttccccttgttattttttttttcccttttgat-cattacggaattatggttgcagcttttgatcctgatagttttttcttctatgcgcatttgttgatctctacag------

upper sequence: GLYMA15G20400.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv16s0050g01460.t01 (Vitis vinifera), 5'ss of exon 3
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctac-aattgcctatgta-actgatatattttcattccttttattttag------------------------
|  ||||| ||||||||  |||||||  | || || |||||||||||    || |||||||| || |||||||||||||| |||||||||||||||||||||||| |   ||  |||| || ||||    | |  |    |     | |||||| || ||| | |   || |||| |   |||   || |||  |||   |  || |  || | |||||||                           
AGCATTCTTGGATTAGAATCTGGAGCTTCAGATTCAGAAATAAAGAAGGCATACAGGAGACTCTCGATTCAATACCATCCTGATAAAAATCCGGATCCAGgttgagg---ttctagttcttcagttaatatgtgttccttagttttactttgat-ttagcaagtactgcgtcttcttttgaatcatctgtgtttactatcaatttctttttgcatttatttatttatctttttttttttgttttccag

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|193549814|gb|FK507509.1|FK507509
EST:     GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAG                         AGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
genomic: GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtg ... tttattttagAGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
EST: gi|192306292|gb|FG996878.1|FG996878
EST:     GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAG                         AGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
genomic: GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtg ... tttattttagAGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
EST: gi|193628757|gb|FK577257.1|FK577257
EST:     GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAG                         AGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
genomic: GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtg ... tttattttagAGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
EST: gi|193322161|gb|FK284939.1|FK284939
EST:     TATAGGAGACTTTCTATTCAATACCATCCAGATAAAAAATCCGGATCCAG                         AGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
genomic: TATAGGAGACTTTCTATTCAATACCATCCAGATAAAAA-TCCGGATCCAGgttgaaggtg ... tttattttagAGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
EST: gi|11274682|gb|BF325019.1|BF325019
EST:     GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGGTTGAAG                   
genomic: GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCC-------AGgttgaaggtg ... ttta
EST: gi|6724522|gb|AW308921.1|AW308921
EST:     GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAG                         AGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA
genomic: GTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtg ... tttattttagAGGCACACAAGTACTTCGTTGAGTACATTGCCAAAGCTTATCAAGCTCTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATTCTAGGATTAGAGCCTGGAGCGGCTGAGTCTGAAATAAAGAAAAAGTATAGGAGACTTTCTATTCAATACCATCCAGATAAAAATCCGGATCCAGgttgaaggtgtttcagttgtttagttttcttattgttgcaatgcaaattttgatgtttgcaggaatgtcggcttcctacaattgcctatgtaactgatatattttcattccttttattttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA