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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTTGCTTTGTATTTCGCCGCAGCAACAACATGCTGTACCCGCGGGAGGACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatcccttgttcgtccttagatttgtccattattttccagattttgttattgattcggggaaaccctaggttcccttagggagctggggccaggttg...

Basic information

species Zea mays
transcript GRMZM5G898768_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G898768_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g42395.2 (Oryza sativa), 5'ss of exon 2
TCTTTGCTTTGTATTTCGCCGCAGCAACAACATGCTGTACCCGCGGGAGGACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatc--ccttgttcgtc--cttagatttgt-ccattattttccagattttgttattgattcggggaaaccctaggttcccttagggagctggggccaggttg
                           ||||||||| ||||||||||||||||||||||||| |||||| || ||||| ||| |  | ||||||||  ||||||||   |||||||| ||  || |||||  |    || |      | | | || | | |      |  ||||||||||   || ||||  | |||  |     
---------------------------CAACATGCTCTACCCGCGGGAGGACAAGGAGACGCACACCCTGCTCTACGCCTGCAATTCCTGCGAGCACCAGgtggatttgccttgttcatcggctcagattaatatggttttggattgggtgtggtaaataaactcttgggaccctaggttggattggggattttggggaa-----

upper sequence: GRMZM5G898768_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g42395.1 (Oryza sativa), 5'ss of exon 2
TCTTTGCTTTGTATTTCGCCGCAGCAACAACATGCTGTACCCGCGGGAGGACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatc--ccttgttcgtc--cttagatttgt-ccattattttccagattttgttattgattcggggaaaccctaggttcccttagggagctggggccaggttg
                        || ||||||||| ||||||||||||||||||||||||| |||||| || ||||| ||| |  | ||||||||  ||||||||   |||||||| ||  || |||||  |    || |      | | | || | | |      |  ||||||||||   || ||||  | |||  |     
------------------------CAGCAACATGCTCTACCCGCGGGAGGACAAGGAGACGCACACCCTGCTCTACGCCTGCAATTCCTGCGAGCACCAGgtggatttgccttgttcatcggctcagattaatatggttttggattgggtgtggtaaataaactcttgggaccctaggttggattggggattttggggaa-----
















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|211284047|gb|FL264875.1|FL264875
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGCAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|5688821|gb|AI941836.1|AI941836
EST:     ACAAGGAGACGCGCNCCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCCCTGATACTTGTGTGTCCAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|60349982|gb|DN216955.1|DN216955
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|211475863|gb|FL467328.1|FL467328
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|37389271|gb|CF631854.1|CF631854
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|14245653|gb|BG874235.1|BG874235
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|211284046|gb|FL264874.1|FL264874
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGCAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|29130428|gb|CB381132.1|CB381132
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|211284045|gb|FL264873.1|FL264873
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCYTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|211204407|gb|FL049974.1|FL049974
EST:     AAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: AAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|37379929|gb|CF626737.1|CF626737
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
EST: gi|30031636|gb|CB833487.1|CB833487
EST:     ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAG                         GAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT
genomic: ACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatccct ... atgtgaacagGAGATTGCCACTGATACTTGTGTGTACAAAAGGGTTATCCGTAAGCCTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTTGCTTTGTATTTCGCCGCAGCAACAACATGCTGTACCCGCGGGAGGACAAGGAGACGCGCACCCTCCTGTACGCGTGCCAAACGTGCGAGCATGAGgtggatcccttgttcgtccttagatttgtccattattttccagattttgttattgattcggggaaaccctaggttcccttagggagctggggccaggttg

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA