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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtccggttttattactgttgctttggatggtgttggaatatctgtgcacatctatcacctttttgttacttgtcgctgtctgctacagtcacactgatgttttgtgccgcccctattatttgctag

Basic information

species Zea mays
transcript GRMZM5G834205_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g01740.2 (Oryza sativa), 5'ss of exon 8
GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtccggttttattactgttgctttggatggtgttggaatatctgtgcacatctatcacctttttgttacttgtcgctgtctgctacagtcacactgatgttttgtgccgcccctattatttgctag
|||||||| ||||| ||||||||||||||||| |||||||| || ||||| || || ||||||||||| || ||||||||||||||||| | ||||  | ||  |  || |  |    ||  | |   | |     | ||  ||  | |  | ||| | |   |  ||| | |       | ||| |||  | | | |  ||     ||  |||||||
GGAGCAACTGATGAGTTTGTGTTGGATCTTGTGGAGCAATGCACATTTCAAAAACAGCGAATAATGCATCTAGTTATGACATCAAGgtaagtgtccactgtt--tggtgctcttcaatatcttttgacattgctccttca-gtccgtgatatgtttataa---gcagctattt-------ttacattgacatat-gagttgctatcctttgttgctag

upper sequence: GRMZM5G834205_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT5G63640.1 (Arabidopsis thaliana), 5'ss of exon 9
GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtccggttttattactgttgctttggatgg--tgttggaatatctgtgcacatctatcacctttttgttacttgtcgctgtctgctacagtcacactgatgttttgtgccgcccctattatttgctag
|| ||||  ||||| |||    | |||||||||||||||||| ||||||||||  | ||  |||||||||| || |||||||| ||| |    ||   || | |  || ||| ||| || ||  ||||  || |  | | |   || |  |      | | |        ||| |  | |||                                      
GGGGCAAAAGATGAGTTTACTCTTGATCTTGTCGAGCAATGTTCGTTTCAGAAAGAGCGCGTAATGCACCTCGTCATGACATCGAGgca--aatc---ttctttctctcttggtttagagggcatgttaaaagaatttttcttttcaagta------tatcaaccaattttgttta-tgcag--------------------------------------
















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|71421501|gb|DR805467.1|DR805467
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|149059924|gb|EE157051.2|EE157051
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|149088092|gb|EE287276.2|EE287276
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|78107222|gb|DV525640.1|DV525640
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|50325446|gb|CO520572.1|CO520572
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|74245587|gb|DT653501.1|DT653501
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|149105965|gb|EE291598.2|EE291598
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|71428013|gb|DR809063.1|DR809063
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|211276223|gb|FL230638.1|FL230638
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|71326004|gb|DR799684.1|DR799684
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAACGGATGAATTTGTGTTGGATCTTGTCGAGCAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtccggttttattactgttgctttggatggtgttggaatatctgtgcacatctatcacctttttgttacttgtcgctgtctgctacagtcacactgatgttttgtgccgcccctattatttgctag

- - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA