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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctatacatctgtgtccatcactagtgtagggtagagtcgtatatgaactaccaaaccatgcgacaggttggtgacctttgtttcctaatcgtgcag

Basic information

species Zea mays
transcript GRMZM2G160430_T01
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160430_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g49270.1 (Oryza sativa), 5'ss of exon 16
ATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccat--ctatacatctgtg-tccatcactagtgtag-ggtagagtcgtatatgaactaccaaaccatgcgacaggttggtgacctttgtttcctaatcgtgcag-------------------
|||||| || | ||||||||||| ||||| || ||||||||| | || |||||||||||||||||||||||||| ||| | || | |||||| |||| |||| |||   | ||| ||| || ||  ||  |  || || || |  ||  | |  |     | | || |    | |  |  |           |     || |||                     
ATCAAGAGTCTCGCAGGAAGCTTTGCGACGCTCGCCAACTGGCTTACATCCTTTGGAATAACAATGACAGCAAACTTGATGCTTAGCTGGAGTGCTGGAGgtacatacttctacttctctgatctctctttcctgcagtggaattgttcttttcgttgagcgagactagagtagaattctgaatatccaacctgacgctcatgctatcttcttaaacatcaacag

upper sequence: GRMZM2G160430_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g49260.1 (Oryza sativa), 5'ss of exon 16
ATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctatacatctgtgtccatcactagtgtagggtagagtcgtatatgaactaccaaaccatgcgacaggttggtgacctttgtttcctaatcgtgcag
|||||| || | |  |||||||| ||||| |||||||||  | | || ||||  | |||||||||||||||||||||| | || | |||||| |||| |||||| | | |  ||     |||     ||    ||  || | |    | ||||||     ||| ||  | | |||    |  |||  ||   | |    |||
ATCAAGAGTCTTGGGGGAAGCTTTGCGACACTTGCCAACATGCTTACATCCTGGGCAATAACAATGACAGCAAATTTGTTACTCAGCTGGAGTGCTGGAGgtccgtatttctataaaaatcctctgttacca-agaataaaat----tctgaactgatttacc-tgataaaagttaa--atattttattttaatttcaacag
















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|44900209|gb|CK826754.1|CK826754
EST:     CTGAACTGGAGCGCTGCAG                         GTTCATTTGCCTCCTACATGACGGTGAGTGCTTTGACTCTCGTCTTCGTCA
genomic: CTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
EST: gi|5915334|gb|AW052975.1|AW052975
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAG                         GTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
EST: gi|101387701|gb|EB815865.1|EB815865
EST:     CTTTGGAATAACAATGACAGCATATTTGCTTCCGAACTGCAGCGCTGCAG                         GGACATTTGCCTCCTACAT
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACAT
EST: gi|37385615|gb|CF629958.1|CF629958
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAG                         GTACATTTGCCTCCTACATGACGGTGAGTGCTTTGACTCTCGTCTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
EST: gi|113701345|gb|EE678849.1|EE678849
EST:     CTTTGGAAT--CAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAG                         GTACATTTGCCTCCTACATGACGGTGAGTGCTTTGACTCTCGTCTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
EST: gi|37376279|gb|CF624650.1|CF624650
EST:     CTTTGGAATAACTATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAG                         GTACATTTGCCTCCTACATGACGGTGAGTGCTTTGACTCTCGTCTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
EST: gi|148950293|gb|EC895852.2|EC895852
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTTTGAACTGGAGCGCTGCAG                         GTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTTTCGTTTTCGTCA
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCCTCCTACATGATGGTGAGTGCTTTCACTCTCGTCTTCGTCA
EST: gi|5846979|gb|AW000058.1|AW000058
EST:     CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAG                         GTACATTTGCC
genomic: CTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctat ... aatcgtgcagGTACATTTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAGTGTGTGGCAGGAAGCTTCGCGACCCTTGCCAACTGGTTGACGTCCTTTGGAATAACAATGACAGCAAATTTGCTTCTGAACTGGAGCGCTGCAGgtccatctatacatctgtgtccatcactagtgtagggtagagtcgtatatgaactaccaaaccatgcgacaggttggtgacctttgtttcctaatcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG