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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAAGGCAAGGAAGAAGGCGGAGCTGCAGAAGGGTAGAGAGTTCTTGGAAACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagaggttcattaatgtgctccttttctccgcatccaatttatgtttcaattttatctcgtcatgtgcaggacgttcatgaccgaatatgcagtt...

Basic information

species Zea mays
transcript GRMZM2G446108_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G446108_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os04g14790.1 (Oryza sativa), 5'ss of exon 6
GACAAGGCAAGGAAGAAGGCGGAGCTGCAGAAGGGTAGAGAGTTCTTGGAAACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagaggttcattaa-tgtgctccttttctccgcatccaatttatgtttcaattttatctcgtcatgtgcaggacgttcatgaccgaatatgcagtt
|||||||||||| |||||   || || || ||||||| ||| ||| ||||||||||||||||||| ||||| || ||||||   ||||| || |||||||||||||| |  ||    |  |  | | ||||||||| | |  |||     ||   ||  |||||  || | || ||                         
GACAAGGCAAGGCAGAAGCTTGAACTACAAAAGGGTAAAGATTTCCTGGAAACATTCAAGTCATCCAAGAATGCACAATTCAGGGATGGCAAACATAATGgtaagaatattttttccaccttcgtttcttttctccactttgaatagcacttctgatagtatctgttcttttgtag-------------------------

upper sequence: GRMZM2G446108_T03 (Zea mays), 5'ss of exon 6
lower sequence: Vv13s0019g04730.t01 (Vitis vinifera), 5'ss of exon 6
GACAAGGCAAGGAAGAAGGCGGAGCTGCAGAAGGGTAGAGAGTTCTTGGAAACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAA-TGgtaagaagaggttcattaatgtgctccttttctccgcatccaatttatgtttcaattttatctcg-tcatgtgcaggacgttcatgaccgaatatgcagtt--------
 ||    |||||||||||   ||| ||||||||| || ||| |||||||| ||||| ||||||||||  ||||| || ||| |||||||||| || || | ||||| |||   |   |  |    || |  |  ||  | | ||||  | ||  | |   ||  |  ||||  |    |   | ||  |    | |   |||        
-ACCGCACAAGGAAGAAGAAAGAGTTGCAGAAGGCTAAAGAATTCTTGGAGACATTTAAGTCATCTAGAAACGCTCAGTTCTATGATGGGAAACACAAATAgtaagtagacaataccttttacattcatactaaccataactaattctt-ttggagtccaatgacaatcataggttttataattatt-cactgtgttaggttcattaaag
















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|60352738|gb|DN219711.1|DN219711
EST:     AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATG                         GACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
genomic: AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagag ... tcatgtgcagGACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
EST: gi|148946266|gb|EC891566.2|EC891566
EST:     AACATTCAAGTCATTTAAGAACGCCCAATTCCATGATGGGAAGCATAATG                         GACGTTCATGACCGAATATGCAGTTTTTTGAATAAGTGTTGATTTTACACA
genomic: AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagag ... tcatgtgcagGACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
EST: gi|211014939|gb|FL077052.1|FL077052
EST:     AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATG                         GACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTATACA
genomic: AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagag ... tcatgtgcagGACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
EST: gi|71760898|gb|DR958835.1|DR958835
EST:     AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATG                         GACGTTCATGACCGAATATGCAGTTTTTTGAATAAGTGTTGATTTTACACA
genomic: AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagag ... tcatgtgcagGACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
EST: gi|211411795|gb|FL441048.1|FL441048
EST:     AACATTCAAGTCATYTAAGAACGCCCAATTCCATGATGGGAAGCATAATG                         GACGTTCATGACCGAATATGCAGTTTTYTGAATAAGTGTTGATTTTATACA
genomic: AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagag ... tcatgtgcagGACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
EST: gi|37379892|gb|CF626714.1|CF626714
EST:     AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATG                         GACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA
genomic: AACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagag ... tcatgtgcagGACGTTCATGACCGAATATGCAGTTTTCTGAATAAGTGTTGATTTTACACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACAAGGCAAGGAAGAAGGCGGAGCTGCAGAAGGGTAGAGAGTTCTTGGAAACATTCAAGTCATCTAAGAACGCCCAATTCCATGATGGGAAGCATAATGgtaagaagaggttcattaatgtgctccttttctccgcatccaatttatgtttcaattttatctcgtcatgtgcaggacgttcatgaccgaatatgcagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC