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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaataccatttctgaaattgactttattcattcaacaatcag

Basic information

species Glycine max
transcript GLYMA13G20780.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os02g41590.1 (Oryza sativa), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtt-taatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaa---taccattt--ctgaaattgactttattcattca-acaatcag----
|||||||||| | || ||||| ||||||||||| |||||||| |||||||| || ||||| |||||||||||||||||      |  || |||||| |  || |||| |||   | |   |     ||||  || ||  ||  |    |  |  |   |  |||  ||     |  ||  |  || |  | | |||  |     || ||  || |    
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGTTGCATTGGAAAGGATAAGTTTGGTGAGGAGATGAAGAAGAATGCCCAAGCTGCTGGTGTTACTgttagttctaaatctctctctctctctctctctttttcatggcatctgatgcaataa-tatcctacagtggcttgtcaactaactaaggtggtcttgctcttgacacacgctcggttag

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g43750.2 (Oryza sativa), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAAAGgtaagtttaatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaataccatttctgaaattgactttat--tcattcaacaatcag
             || ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| || | |||||  |  ||    |||   || |   ||  ||    |    | |    |  || |  |  |  |   ||  |      ||||| |||   || || ||||     
----------ATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAATgcaagttataagttcctctttatgttttaaatttcttccatttttatgcctcttcactcagttgcaccactgcacatactgccttgaccttaccatctttaaacag----

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os04g43750.1 (Oryza sativa), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAAAGgtaagtttaatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaataccatttctgaaattgactttat--tcattcaacaatcag
|||||| ||    || ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||||| | | | |||    | |||||| || | |||||  |  ||    |||   || |   ||  ||    |    | |    |  || |  |  |  |   ||  |      ||||| |||   || || ||||     
GATGCTCCAGATTCCTGGTGCAACAAGTTACATGGGTTGCATTGGGAAGGACAAGTTCGGTGAGGAGATGAAGAA-AGACGCACAAACCGCTGGTGTTAATgcaagttataagttcctctttatgttttaaatttcttccatttttatgcctcttcactcagttgcaccactgcacatactgccttgaccttaccatctttaaacag----

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G540538_T02 (Zea mays), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaataccatttctgaaattgactttat-tcattcaacaatcag
|||||||||| | || ||||| ||||||||||| || ||||| ||||||||||| ||||| ||||| |||||||| ||     | ||  | | || |   || | | | |  || | || |   || || |    ||    ||  |   | |||  |  |  | | |  ||   |  || | || | ||| || || |   | | ||||
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGAAAGGACAAGTTTGGTGAGGAAATGAAGAAAAA-----CGCTCAA-GCTGCAGGAGTTACTgttagtttttaatctca-ttgtcttcatgttactttagacagttttgttgc-aatttattggttaat-tcactcatatggccttgatgtcgtcgcatactcag

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G135132_T01 (Zea mays), 5'ss of exon 5
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagttt-aatcttgtgatttggcttctcctttct-ttgtgataagctactctgtgcctgacctttagaataccat--ttctgaaattgac-tttattcattcaacaatcag
|||||||||| | || ||||| ||||||||||| || ||||| || |||||||| ||||| |||||||||||||| ||   |  |  ||  || || |  || ||||| |||||  |  | |   | || ||||     || ||   ||  | | |   || |   | || ||   |     |||  ||| |  |||   | |||        
GATGCTTCAAACTCCTGGTGCAACAAGTTACATGGGATGCATTGGGAAGGACAAGTTTGGTGAGGAGATGAAGAAAAATGCTCAAGCTGCAGGAGTTACTgttagttttaatctcatcttcttcatgctactttagacagtaatgttctgatttat---tggctaattgactaatgtggccttgatgttggcgcttacctactcag-------

upper sequence: GLYMA13G20780.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G089767_T01 (Zea mays), 5'ss of exon 3
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACAC-TTGATGGTGTAAAGgtaagtttaatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaataccatttctgaaattgactttattcattcaacaatcag
||||||||||   || |||||  |||||||||| |||||||| || ||||| || ||||| ||||||||||| || ||||| |||   || |||| | || |||||||  |              || |  ||||||| ||  |   |||    |  |  | ||    | ||  |   |   |      | ||| ||  ||        
GATGCTTCAAATTCCTGGTGCATCAAGTTACATTGGTTGCATCGGGAAGGATAAGTTTGGTGAGGAGATGAAAAA-AAATGCACAAGCTGCTGGTATTAATgtaagttgta------aggccccttttttttttctttatggcacattacctcatttcacaactagcaactataaccccgcca------tctatgcaaccag-------

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|209708530|gb|BW668141.1|BW668141
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|209710379|gb|BW681278.1|BW681278
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|13311384|gb|BG405035.1|BG405035
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|192324906|gb|FK016092.1|FK016092
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|213598835|gb|DB968306.1|DB968306
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|209711575|gb|BW676820.1|BW676820
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|193667347|gb|FK609753.1|FK609753
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|209711086|gb|BW681150.1|BW681150
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTG
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTG
EST: gi|151405346|gb|EV275160.1|EV275160
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|207703119|gb|GD684897.1|GD684897
EST:     GAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: GAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|151404672|gb|EV274486.1|EV274486
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|11687342|gb|BF594982.1|BF594982
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|213611486|gb|DB959196.1|DB959196
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|9987590|gb|BE661698.1|BE661698
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|213597865|gb|DB958246.1|DB958246
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|151405163|gb|EV274977.1|EV274977
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|19937792|gb|BQ081423.1|BQ081423
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|12773014|gb|BG237941.1|BG237941
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|14126129|gb|BG790567.1|BG790567
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|308098710|gb|HO760451.1|HO760451
EST:     ACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|213591667|gb|DB969767.1|DB969767
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|213587888|gb|DB959712.1|DB959712
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|213605470|gb|DB964609.1|DB964609
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|208273170|gb|GE070092.1|GE070092
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTGGAACTTGTGCTGTTTGT
EST: gi|4395913|gb|AI494910.1|AI494910
EST:     ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAG                         GTTAACTATTATGAAATCGACAATACACCTACTG
genomic: ACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaa ... caacaatcagGTTAACTATTATGAAATCGACAATACACCTACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTTCAAGCACCAGGTGCCACAAGTTACATAGGTTGCATAGGAAAGGACAAATTTGGAGAGGAGATGAAGAAGAAATGTACACTTGATGGTGTAAAGgtaagtttaatcttgtgatttggcttctcctttctttgtgataagctactctgtgcctgacctttagaataccatttctgaaattgactttattcattcaacaatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA