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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatcccctctccactatcacactcttggcccttgatccttattagcccaaccacacccccacacgccatatttgttgcagtatctgaacttgattctctctttggttatgcag

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 11
TCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatcccctctccactatcacactcttggcccttgatcctt-------------attagcccaacc-----acacccccacacgcc----------------atatttgttgcagtatct---gaacttgatt------ctctctttggttatgcag
||| |||||||||||| | |||||||||||||| ||||| ||||||||||| ||| | ||||||||||||||||| |||||    ||||| |||||  ||||| |||    |||  |   |  | ||  |     ||  ||| |             ||||||  ||       |||| |   |  |||                |||||||  ||| |  ||   | || | |||      ||   ||||||| |||||
TCCAATGGGAGAATCATCTGTGGACTGTGGCAGCCTTGCATCCATGCCTGAGATTTCATTCACCATTGGAGGCAAAAAGTTTGCACTGAAGCCAGAAGAGgtgcgatgatttctttatggtttctcttcttttttttcttcccttgggtgcatctagattagctgaaaagttggacacgcttgccggcccatctagtttgtgtagatatttgacgcactggcttgagcacataatttactctcttcttttggttgtgcag
















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|213167748|gb|FM184910.1|FM184910
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|67017226|gb|CO445975.1|CO445975
EST:     CATTGCGTTCACCATTTGGAG-CAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTNGGTGAAG-ACANGCTGCCCANTGCATCANCNGATT
genomic: CATTGCGTTCACCATT-GGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTT-GGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATT
EST: gi|86856157|gb|DY307168.1|DY307168
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|33096169|gb|CF056163.1|CF056163
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|213179239|gb|FM192959.1|FM192959
EST:     GCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: GCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|211092713|gb|FK945553.1|FK945553
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|31354952|gb|CD439309.1|CD439309
EST:     ACATTGCGTTCACCATTGGAGGCAATAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|67038995|gb|CO465250.1|CO465250
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|32918238|gb|CF023050.1|CF023050
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGGTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|213179820|gb|FM194304.1|FM194304
EST:     GGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: GGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|32912159|gb|CF016971.1|CF016971
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|16919046|gb|BM074015.1|BM074015
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|211361839|gb|FL432808.1|FL432808
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|21621076|gb|BQ619082.1|BQ619082
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|116816042|gb|EC858742.1|EC858742
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCCAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAA
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAA
EST: gi|33096659|gb|CF056653.1|CF056653
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|33096356|gb|CF056350.1|CF056350
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|47962340|gb|CN845049.1|CN845049
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|60337171|gb|DN204144.1|DN204144
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|38229766|gb|CF920079.1|CF920079
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
EST: gi|61119127|gb|DN560088.1|DN560088
EST:     ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAATCAGAGCAG                         TACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC
genomic: ACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatccc ... ggttatgcagTACATTCTGAAGGTTGGTGAAGGACAGGCTGCCCAGTGCATCAGCGGATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCGATGGGAGAATCAGCCGTGGACTGTGGCAGTCTTGCGTCCATGCCTGACATTGCGTTCACCATTGGAGGCAAGAAGTTCAAGCTGAAACCAGAGCAGgtgtgatcccctctccactatcacactcttggcccttgatccttattagcccaaccacacccccacacgccatatttgttgcagtatctgaacttgattctctctttggttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG