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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcatcatgctatttttttttagctttttgtgcatctgcttggagatattgttgtc...

Basic information

species Zea mays
transcript GRMZM2G085670_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085670_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 5'ss of exon 8
CAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcat-catgctatttttttttagctttttgtgcatctgcttggagatatt--gttgtc
||||||||||||||| |||| |||||||||||||  ||||||||| ||| |||||||||||||||||||||||||||  |||||||||| |||||||| | |      | |||| |   | | | ||   ||   || | | |||  |||||||   |    ||| ||  | |   ||  | || |   |  || 
CAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg---tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G085670_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 8
--------CAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcat-catgctatttttttttagctttttgtgcatctgcttggagatat--tgttgtc
        ||||||||||||||| |||| |||||||||||||  ||||||||| ||| |||||||||||||||||||||||||||  |||||||||| |||||||| | |      | |||| |   | | | ||   ||   || | | |||  |||||||   |    ||| ||  | |   ||  | || |   |  || 
AATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg---tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G085670_T04 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 5'ss of exon 8
CAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcat-catgctatttttttttagctttttgtgcatctgcttggagatatt--gttgtc
   |||||||||||| |||| |||||||||||||  ||||||||| ||| |||||||||||||||||||||||||||  |||||||||| |||||||| | |      | |||| |   | | | ||   ||   || | | |||  |||||||   |    ||| ||  | |   ||  | || |   |  || 
---GCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg---tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

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|86473889|gb|DY240259.1|DY240259
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211111835|gb|FL481580.1|FL481580
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|71330909|gb|DR802251.1|DR802251
EST:     AATCTGTAGGAATAATGGATTTTGAAGAGGACCTGTGTC-GACCAAAGAG                         GAGGCGATCA-CCACTGGCG
genomic: AATCTGTAGGAATAATGGATTTTGAAGAGGACC-GTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGA-CAACCACTGGCG
EST: gi|16925930|gb|BM078998.1|BM078998
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|71306428|gb|DR789361.1|DR789361
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211195517|gb|FL100641.1|FL100641
EST:     GGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|33092814|gb|CF052808.1|CF052808
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211193128|gb|FL100640.1|FL100640
EST:     GAATCTGTAKGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAKCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|74236689|gb|DT644603.1|DT644603
EST:     GAATCTGTAGGGATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACTACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|211111836|gb|FL481581.1|FL481581
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|60359667|gb|DN226640.1|DN226640
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
EST: gi|78024318|gb|DV492705.1|DV492705
EST:     GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAG                         GAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT
genomic: GAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaat ... gatattgcagGAGGCGACAACCACTGGCGTAGTTTCAATTAAGCCCTTACAAATCTCTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGCAGACATCGACATACGAGGGCATGACGACTACCTCTCTGAATCTGTAGGAATAATGGATTTTGAAGAGGACCGTGTCCGACCAAAGAGgtaataaaatacagtgcactctaggttttgttgtgcggttatgtatcatcatgctatttttttttagctttttgtgcatctgcttggagatattgttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA