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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_T03
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|101391432|gb|EB817651.1|EB817651
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|78077690|gb|DV506124.1|DV506124
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|149050347|gb|EE155591.2|EE155591
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|84970062|gb|DW468434.1|DW468434
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|37375076|gb|CF623952.1|CF623952
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACGCTGGTATCA-A-GCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|71302875|gb|DR787549.1|DR787549
EST:     AATGTACG-TTCAGAAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: AATGTACGTTTCAG-AAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|71761883|gb|DR959820.1|DR959820
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|86472430|gb|DY238800.1|DY238800
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|48690727|gb|CO049262.1|CO049262
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGG-AGTCACAAGCTATAGAGCTAAATGAAGAGCTACATA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTA-TCACAAGCTATAGAGCTAAATGAAGAGCTACATA
EST: gi|50325059|gb|CO520185.1|CO520185
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|211390578|gb|FL303487.1|FL303487
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|37394180|gb|CF634361.1|CF634361
EST:     CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAG                         GGATGAAACGCTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
genomic: CAATGTACGTTTCAGAAGCAACGAATAATGCACCTTGTTATGACATCAAGgtacgggtcc ... tatttgctagGGATGAAACACTGGTATCACAAGCTATAGAGCTAAATGAAGAGCTACATAA
EST: gi|76291817|gb|DV031385.1|DV031385
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