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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatattgttgtc...

Basic information

species Zea mays
transcript GRMZM2G171745_T05
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 8
AATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatat--tgttgtc
||||||||||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||| ||| | | ||   | |  | |  | | | || | ||   ||   | |  |  |||||||  || |||   ||  | |   ||  | || |   |  || 
AATTTAAGCAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg--tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g30840.1 (Oryza sativa), 5'ss of exon 8
AATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatatt--gttgtc
        ||||||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||| ||| | | ||   | |  | |  | | | || | ||   ||   | |  |  |||||||  || |||   ||  | |   ||  | || |   |  || 
--------CAGGCAGACATCGACTTACGGGGGCATGACGACTTTCTCTCTGAACCTGGAGGAATAATGGATTTTGAAGAGGACCGCATCCGACCAAAAAGgtaatatattttttctctctcttg--tgggtttggatttgcttaccttacataatatttttaaattttgtttagtatagcctgttaaaaatgtaaggcagtt

upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g30840.2 (Oryza sativa), 5'ss of exon 8
AATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatatt--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|50339562|gb|CO534688.1|CO534688
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCCCCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|37419216|gb|CF647286.1|CF647286
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|149027222|gb|EE046433.2|EE046433
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|60398630|gb|DN231446.1|DN231446
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|78109059|gb|DV527476.1|DV527476
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|28986944|gb|CB351386.1|CB351386
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|113702753|gb|EE680257.1|EE680257
EST:     GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: GAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA
EST: gi|211477594|gb|FL101253.1|FL101253
EST:     AATCTGGAGGAATAATGGATTTTGAAGAAGGACCGCGTCCGACCAAAAAG                         GAGGAGGCAACCNCCGGCGNAGTTTCAATTAGCCCTTACCAATCTCTCCCA
genomic: AATCTGGAGGAATAATGGATTTTGAAGA-GGACCGCGTCCGACCAAAAAGgtgataaaat ... gatattgcagGAGGAGGCAACCACCGGCGTAGTTTCAATTAGCCCTTACCAATCTCTCCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTTAAGCAGGCAGACATTGACTTACGGGGGCATGACGAGTTTCTCTCTGAATCTGGAGGAATAATGGATTTTGAAGAGGACCGCGTCCGACCAAAAAGgtgataaaatgttgggcaccataggtttgttatgtagttatgtattatcctgataatttttagcttgtgtggcgtgcatctgtttggagatattgttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA