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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgagacctgatccccctcccgtcgcgtacaatttctagggtttatgcgttccggagtggaattcaggagacttgtttggggggaattttgattgt...

Basic information

species Oryza sativa
transcript LOC_Os01g71300.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G155334_T01 (Zea mays), 5'ss of exon 2
----------GGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgta-tgtgagacctgatccccctcccgtcgcgtacaatttctagggtttatgcgttccggagtggaattcaggagact---tgtttggggggaattttgattgt
          |||||||| || | ||||||||| ||| |||  ||||          |||||||||||||||| ||||||||||||| ||| | || |||||||||||||||| |||   |  ||| ||||||| | || | |   | |   || ||| |||  ||  |  || |  || |   | ||    ||  ||| | ||     |  | 
CTGGCTCTCGGGCCTCACCTGTACCGACGAGAATTTCATCATGAAGG----------GCGCGCCGCCGCCGCCAACGGCATCGCCCTTGTCACGCCTGACACCTCCCCACgtaatgtcgaaattgaaccccctctcctc-cctttgactgacagcgtt-atgt-tttagttgtagggtttacatgcctgcccgtaggggtgaaaacgaaaacg-

upper sequence: LOC_Os01g71300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G046558_T01 (Zea mays), 5'ss of exon 2
GGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgagacctgatcc-------ccctcccgtcgcgtacaatttctagggtttatgcgttccggagtggaattcaggagacttgtttggggggaattttgattgt
|| ||||| |||| ||||||||| ||| |||  ||| ||||||| |||||||||||||| |||||||||||||||||||| || || |||||||||||||||||||   |  ||| ||       |||||     |   |   |||||||||||||||| | ||    ||   | | | |||  |  ||  |     || |      
GGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCGGCGCCCAGCGCGCCGCCGCTGCCCACGGCATCGCCCTCGTGGCACCTGACACCTCCCCACgtatgtcgaaattgagccaactcctccctctgactgtacagggtttctagggtttatgcctgcccatctgtg-tccggaaga--tacttacgattccttctct----

upper sequence: LOC_Os01g71300.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G108369_T01 (Zea mays), 5'ss of exon 2
GGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgagacctgatccccctcccgtcgc-----gtacaa--tttctagggtttatgcgttccggagtggaattcaggagacttgtttggggggaattttgattgt
|| ||||| |||| ||||||||| ||| |||  ||| || |||| |||||||||||||| ||||||| |||||||||||| || || |||||||||||||||||||   |  ||| || |||||   | |     |||||   |||||||||||||||| | |     ||   | | | |||  |  ||  |     || |      
GGTCTCACCTGCACCGACGAGAATTTCATCATAAAGTCCAGCGCCCAGCGCGCCGCCGCTGCCCACGACATCGCCCTCGTGGCACCTGACACCTCCCCACgtatgtcgaaattgagccacctcctccctctgactgtacagggtttctagggtttatgcctgctcatctgtg-tccggaaga--tacttacgattccttctct----

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|89172386|gb|CI721445.1|CI721445
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88670559|gb|CI724675.1|CI724675
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88673403|gb|CI727516.1|CI727516
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88673631|gb|CI727744.1|CI727744
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88676329|gb|CI730442.1|CI730442
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88676307|gb|CI730420.1|CI730420
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|33793279|gb|CF322520.1|CF322520
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88672556|gb|CI726672.1|CI726672
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88667436|gb|CI722175.1|CI722175
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|58591479|gb|CF989787.1|CF989787
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|58604050|gb|CK014578.1|CK014578
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|89171382|gb|CI720441.1|CI720441
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88669850|gb|CI723966.1|CI723966
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88675254|gb|CI727369.1|CI727369
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
EST: gi|88672977|gb|CI727092.1|CI727092
EST:     CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCAC                         GTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG
genomic: CGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgaga ... cttcatgcagGTGGGCTTAATATAGAGGGAGAGGCAGACAGTTGGGATTTTGGTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCTCACGTGCAACGACGAGAACTTCGTCACCAAGGCCGGCGCGCAGCGCGCCGCCGCCGCCCACGGCATCGCCCTCGTCGCCCCCGACACCTCCCCACgtatgtgagacctgatccccctcccgtcgcgtacaatttctagggtttatgcgttccggagtggaattcaggagacttgtttggggggaattttgattgt

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